normalised logo rendering (JAL-958)

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index b63e600..d56fb01 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -321,14 +321,16 @@ public class AAFrequency
     }
     ;
     jalview.util.QuickSort.sort(vl, ca);
-    rtnval[0] = 1;
+    rtnval[0] = 2;
+    rtnval[1]=0;
     for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
     {
       if (((char[]) ca[c])[0] != '-')
       {
         rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
-        rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+        rtnval[rtnval[0]] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
                 : 0]);
+        rtnval[1]+=rtnval[rtnval[0]++];
       }
     }
     return rtnval;