X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=8dd8994d8f61f93d7045b9513c27568bc381ce96;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=eaf2a5f96e10ce729406c13d848ff438439deac8;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index eaf2a5f..8dd8994 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -70,7 +70,7 @@ public class ClustalxColourScheme
     int res;
     int i;
     int j = 0;
-    char [] seq;
+    char[] seq;
 
     while (j < seqs.size())
     {
@@ -86,7 +86,7 @@ public class ClustalxColourScheme
         }
         else
         {
-          res =  ResidueProperties.aaIndex[seq[i]];
+          res = ResidueProperties.aaIndex[seq[i]];
         }
 
         cons2[i][res]++;
@@ -249,8 +249,7 @@ public class ClustalxColourScheme
   {
     Color currentColour;
 
-
-    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(c, j)))
+    if (cons2.length <= j || (threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
@@ -264,13 +263,13 @@ public class ClustalxColourScheme
       return currentColour;
     }
 
-  for (int k = 0; k < ResidueColour[i].conses.length; k++)
-  {
-    if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+    for (int k = 0; k < ResidueColour[i].conses.length; k++)
     {
-      currentColour = ResidueColour[i].c;
+      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
+      {
+        currentColour = ResidueColour[i].c;
+      }
     }
-  }
 
     if (i == 4)
     {
@@ -280,8 +279,10 @@ public class ClustalxColourScheme
       }
     }
 
-    if(conservationColouring)
+    if (conservationColouring)
+    {
       currentColour = applyConservation(currentColour, j);
+    }
 
     return currentColour;
   }