From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 18 Mar 2015 20:32:18 +0000 (+0000)
Subject: JAL-1680 small tidy
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=f5448ec3a478b5567cd2844e47a01398af63daee

JAL-1680 small tidy
---

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 5cf4e30..3c8274e 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -420,7 +420,7 @@ public class StructureFrequency
          * ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; } }
          * else {
          */
-        Object[] ca = new Object[625];
+        int[][] ca = new int[625][];
         float[] vl = new float[625];
         int x = 0;
         for (int c = 65; c < 90; c++)
@@ -436,14 +436,18 @@ public class StructureFrequency
         jalview.util.QuickSort.sort(vl, ca);
         int p = 0;
 
+        /*
+         * profile[1] is {total, ungappedTotal}
+         */
+        final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+                : 0];
         for (int c = 624; c > 0; c--)
         {
           if (vl[c] > 0)
           {
-            tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
-                    : 0]);
-            mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
-                    + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval)
+            tval = (vl[c] * 100f / divisor);
+            mouseOver += ((p == 0) ? "" : "; ") + (char) ca[c][0]
+                    + (char) ca[c][1] + " " + fmt.form(tval)
                     + "%";
             p++;
 
@@ -500,14 +504,14 @@ public class StructureFrequency
     int valuesCount = 0;
     rtnval[1] = 0;
     int offset = 2;
+    final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
     for (int c = 624; c > 0; c--)
     {
       if (vl[c] > 0)
       {
         rtnval[offset++] = ca[c][0];
         rtnval[offset++] = ca[c][1];
-        rtnval[offset] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
-                : 0]);
+        rtnval[offset] = (int) (vl[c] * 100f / divisor);
         rtnval[1] += rtnval[offset++];
         valuesCount++;
       }