X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=00f8f6f6bb1c597eb1af80cf05d222367bc12052;hb=c1e70ea0a01d2c916675aa8020970c6696d0dba5;hp=e5efb1a27de5a5a2ad401ced137de663ab75afe2;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index e5efb1a..00f8f6f 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -24,6 +24,8 @@ import java.util.StringTokenizer;
 public class UserColourScheme
     extends ResidueColourScheme
 {
+  Color [] lowerCaseColours;
+
   protected String schemeName;
 
   public UserColourScheme()
@@ -54,6 +56,11 @@ public class UserColourScheme
     return colors;
   }
 
+  public Color[] getLowerCaseColours()
+  {
+    return lowerCaseColours;
+  }
+
   public void setName(String name)
   {
     schemeName = name;
@@ -138,11 +145,34 @@ public class UserColourScheme
         st2 = new StringTokenizer(residues, " ,");
         while (st2.hasMoreTokens())
         {
-          int colIndex =
-              ( (Integer) ResidueProperties.aaHash.
-               get(st2.nextToken())).intValue();
-
-          colors[colIndex] = getColourFromString(colour);
+          token = st2.nextToken();
+
+          if (ResidueProperties.aaIndex[token.charAt(0)]==-1)
+            continue;
+
+          int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
+
+          if(token.equalsIgnoreCase("lowerCase"))
+          {
+            if (lowerCaseColours == null)
+              lowerCaseColours = new Color[23];
+            for (int i = 0; i < 23; i++)
+              if (lowerCaseColours[i] == null)
+                lowerCaseColours[i] = getColourFromString(colour);
+
+              continue;
+          }
+
+          if(token.equals(token.toLowerCase()))
+          {
+            if(lowerCaseColours==null)
+            {
+              lowerCaseColours = new Color[23];
+            }
+            lowerCaseColours[colIndex] = getColourFromString(colour);
+          }
+          else
+            colors[colIndex] = getColourFromString(colour);
         }
       }
     }
@@ -154,4 +184,35 @@ public class UserColourScheme
 
   }
 
+
+
+  public Color findColour(char c, int j)
+  {
+      Color currentColour;
+      int index = ResidueProperties.aaIndex[c];
+
+      if ((threshold == 0) || aboveThreshold(c, j))
+      {
+        if(lowerCaseColours!=null && 'a' <= c && c <= 'z')
+          currentColour = lowerCaseColours[index];
+        else
+          currentColour = colors[index];
+      }
+      else
+      {
+          currentColour = Color.white;
+      }
+
+      if(conservationColouring)
+       currentColour =  applyConservation(currentColour, j);
+
+
+      return currentColour;
+   }
+
+   public void setLowerCaseColours(Color [] lcolours)
+   {
+     lowerCaseColours = lcolours;
+   }
+
 }