From d640a8ce605b836b2e6eb1771994d3baef5c31a0 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 28 Nov 2006 17:18:23 +0000
Subject: [PATCH] CurrentColour must not be accessed by multiple sequence
 renderers

---
 src/jalview/schemes/AnnotationColourGradient.java |    2 +-
 src/jalview/schemes/Blosum62ColourScheme.java     |    2 +-
 src/jalview/schemes/ClustalxColourScheme.java     |    2 +-
 src/jalview/schemes/NucleotideColourScheme.java   |    2 +-
 src/jalview/schemes/PIDColourScheme.java          |    2 +-
 src/jalview/schemes/ResidueColourScheme.java      |    8 ++++----
 src/jalview/schemes/ScoreColourScheme.java        |    2 +-
 src/jalview/schemes/UserColourScheme.java         |    2 +-
 8 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 8367cad..4a78aa1 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -179,7 +179,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
         }
 
         if(conservationColouring)
-         applyConservation(currentColour, j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d3b93bf..f2d2c98 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -82,7 +82,7 @@ public class Blosum62ColourScheme
       }
 
       if(conservationColouring)
-         applyConservation(currentColour, j);
+       currentColour =  applyConservation(currentColour, j);
     }
     else
     {
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index ce30de8..4c20873 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -281,7 +281,7 @@ public class ClustalxColourScheme
     }
 
     if(conservationColouring)
-         applyConservation(currentColour, j);
+      currentColour = applyConservation(currentColour, j);
 
     return currentColour;
   }
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index f36bcad..4afb321 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -78,7 +78,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         }
 
         if(conservationColouring)
-         applyConservation(currentColour, j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index b287384..9bd092e 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -83,7 +83,7 @@ public class PIDColourScheme
       }
 
     if(conservationColouring)
-         applyConservation(currentColour, j);
+      currentColour = applyConservation(currentColour, j);
 
     return currentColour;
   }
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bf83665..b905c45 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -97,7 +97,7 @@ public class ResidueColourScheme implements ColourSchemeI
        }
 
        if(conservationColouring)
-         applyConservation(currentColour, j);
+         currentColour = applyConservation(currentColour, j);
 
 
        return currentColour;
@@ -221,7 +221,7 @@ public class ResidueColourScheme implements ColourSchemeI
     * @return DOCUMENT ME!
     */
 
-   void applyConservation(Color currentColour, int i)
+   Color applyConservation(Color currentColour, int i)
    {
 
      if ((conservation[i] != '*') && (conservation[i] != '+'))
@@ -235,8 +235,7 @@ public class ResidueColourScheme implements ColourSchemeI
          float t = 11 - (conservation[i] - '0');
          if(t==0)
          {
-           currentColour = Color.white;
-           return;
+           return Color.white;
          }
 
          int red = currentColour.getRed();
@@ -261,6 +260,7 @@ public class ResidueColourScheme implements ColourSchemeI
            currentColour = new Color(red, green, blue);
        }
        }
+       return currentColour;
    }
 
 
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index c9f7fc8..4cd9fd3 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -102,7 +102,7 @@ public class ScoreColourScheme extends ResidueColourScheme
         Color currentColour = colors[ ResidueProperties.aaIndex[c] ];
 
         if(conservationColouring)
-         applyConservation(currentColour, j);
+          currentColour =  applyConservation(currentColour, j);
 
         return currentColour;
     }
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 9d61279..c029b31 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -204,7 +204,7 @@ public class UserColourScheme
       }
 
       if(conservationColouring)
-        applyConservation(currentColour, j);
+       currentColour =  applyConservation(currentColour, j);
 
 
       return currentColour;
-- 
1.7.10.2