X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=aa1e2774beed6ad0f0ac5d3ef36c2758fd8e76a5;hb=bbfdb203ce3a889600caa52478478b75ab03809f;hp=c15dba4ed25d52703fdd7d5a19c47a64966888b4;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index c15dba4..aa1e277 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -406,7 +406,7 @@ public class StructureFrequency
   public static int[] extractProfile(Hashtable hconsensus,
           boolean ignoreGapsInConsensusCalculation)
   {
-    int[] rtnval = new int[51]; // 2*(5*5)+1
+    int[] rtnval = new int[52]; // 2*(5*5)+2
     int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
     int[][] pairs = (int[][]) hconsensus
             .get(StructureFrequency.PAIRPROFILE);
@@ -430,15 +430,17 @@ public class StructureFrequency
     }
     jalview.util.QuickSort.sort(vl, ca);
 
-    rtnval[0] = 1;
+    rtnval[0] = 2;
+    rtnval[1] = 0;
     for (int c = 624; c > 0; c--)
     {
       if (vl[c] > 0)
       {
         rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
         rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
-        rtnval[rtnval[0]++] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+        rtnval[rtnval[0]] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
                 : 0]);
+        rtnval[1]+=rtnval[rtnval[0]++];
       }
     }