CurrentColour must not be accessed by multiple sequence renderers

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 8367cad..4a78aa1 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -179,7 +179,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
         }\r
 \r
         if(conservationColouring)\r
-         applyConservation(currentColour, j);\r
+         currentColour = applyConservation(currentColour, j);\r
 \r
        return currentColour;\r
     }\r

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d3b93bf..f2d2c98 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -82,7 +82,7 @@ public class Blosum62ColourScheme
       }\r
 \r
       if(conservationColouring)\r
-         applyConservation(currentColour, j);\r
+       currentColour =  applyConservation(currentColour, j);\r
     }\r
     else\r
     {\r

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index ce30de8..4c20873 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -281,7 +281,7 @@ public class ClustalxColourScheme
     }\r
 \r
     if(conservationColouring)\r
-         applyConservation(currentColour, j);\r
+      currentColour = applyConservation(currentColour, j);\r
 \r
     return currentColour;\r
   }\r

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index f36bcad..4afb321 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -78,7 +78,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         }\r
 \r
         if(conservationColouring)\r
-         applyConservation(currentColour, j);\r
+         currentColour = applyConservation(currentColour, j);\r
 \r
        return currentColour;\r
     }\r

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index b287384..9bd092e 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -83,7 +83,7 @@ public class PIDColourScheme
       }\r
 \r
     if(conservationColouring)\r
-         applyConservation(currentColour, j);\r
+      currentColour = applyConservation(currentColour, j);\r
 \r
     return currentColour;\r
   }\r

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bf83665..b905c45 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -97,7 +97,7 @@ public class ResidueColourScheme implements ColourSchemeI
        }\r
 \r
        if(conservationColouring)\r
-         applyConservation(currentColour, j);\r
+         currentColour = applyConservation(currentColour, j);\r
 \r
 \r
        return currentColour;\r
@@ -221,7 +221,7 @@ public class ResidueColourScheme implements ColourSchemeI
     * @return DOCUMENT ME!\r
     */\r
 \r
-   void applyConservation(Color currentColour, int i)\r
+   Color applyConservation(Color currentColour, int i)\r
    {\r
 \r
      if ((conservation[i] != '*') && (conservation[i] != '+'))\r
@@ -235,8 +235,7 @@ public class ResidueColourScheme implements ColourSchemeI
          float t = 11 - (conservation[i] - '0');\r
          if(t==0)\r
          {\r
-           currentColour = Color.white;\r
-           return;\r
+           return Color.white;\r
          }\r
 \r
          int red = currentColour.getRed();\r
@@ -261,6 +260,7 @@ public class ResidueColourScheme implements ColourSchemeI
            currentColour = new Color(red, green, blue);\r
        }\r
        }\r
+       return currentColour;\r
    }\r
 \r
 \r

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index c9f7fc8..4cd9fd3 100755 (executable)
--- 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] ];\r
 \r
         if(conservationColouring)\r
-         applyConservation(currentColour, j);\r
+          currentColour =  applyConservation(currentColour, j);\r
 \r
         return currentColour;\r
     }\r

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 9d61279..c029b31 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -204,7 +204,7 @@ public class UserColourScheme
       }\r
 \r
       if(conservationColouring)\r
-        applyConservation(currentColour, j);\r
+       currentColour =  applyConservation(currentColour, j);\r
 \r
 \r
       return currentColour;\r