normalised logo rendering (JAL-958)

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

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 42e8847..aa1e277 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -15,6 +15,7 @@
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
+
 package jalview.analysis;
 
 import java.util.*;
@@ -405,7 +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);
@@ -429,15 +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]++];
       }
     }