X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=1342bb273760f0efc2524e1d3e2840ddf30b2f9c;hb=71d8702f4f5f12c9c2f1dcb119091704dc738522;hp=ad3f8d9856e4a62a542f354b60b365ca49ffdae6;hpb=99d5403ff5f28eea4349d2d812efd64ac09e5d44;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index ad3f8d9..1342bb2 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -149,8 +149,8 @@ public class StructureFrequency
           {
             if (sequences[j] == null)
             {
-              System.err
-                      .println("WARNING: Consensus skipping null sequence - possible race condition.");
+              System.err.println(
+                      "WARNING: Consensus skipping null sequence - possible race condition.");
               continue;
             }
 
@@ -195,8 +195,9 @@ public class StructureFrequency
       if (profile)
       {
         // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
-        residueHash.put(PROFILE, new int[][] { values,
-            new int[] { jSize, (jSize - values['-']) } });
+        residueHash.put(PROFILE,
+                new int[][]
+                { values, new int[] { jSize, (jSize - values['-']) } });
 
         residueHash.put(PAIRPROFILE, pairs);
       }
@@ -217,22 +218,23 @@ public class StructureFrequency
       {
         if (canonicalOrWobblePairCount >= otherPairCount)
         {
-          maxResidue = (canonicalOrWobblePairCount - canonical) < canonical ? "("
-                : "[";
+          maxResidue = (canonicalOrWobblePairCount - canonical) < canonical
+                  ? "("
+                  : "[";
         }
         else
         {
           maxResidue = "{";
         }
       }
-      residueHash.put(MAXCOUNT, new Integer(count));
+      residueHash.put(MAXCOUNT, Integer.valueOf(count));
       residueHash.put(MAXRESIDUE, maxResidue);
 
       percentage = ((float) count * 100) / jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
+      residueHash.put(PID_GAPS, Float.valueOf(percentage));
 
       percentage = ((float) count * 100) / nongap;
-      residueHash.put(PID_NOGAPS, new Float(percentage));
+      residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
       if (result[i] == null)
       {
@@ -252,20 +254,21 @@ public class StructureFrequency
         residueHash = new Hashtable();
         if (profile)
         {
-          residueHash.put(PROFILE, new int[][] { values,
-              new int[] { jSize, (jSize - values['-']) } });
+          residueHash.put(PROFILE,
+                  new int[][]
+                  { values, new int[] { jSize, (jSize - values['-']) } });
 
           residueHash.put(PAIRPROFILE, pairs);
         }
 
-        residueHash.put(MAXCOUNT, new Integer(count));
+        residueHash.put(MAXCOUNT, Integer.valueOf(count));
         residueHash.put(MAXRESIDUE, maxResidue);
 
         percentage = ((float) count * 100) / jSize;
-        residueHash.put(PID_GAPS, new Float(percentage));
+        residueHash.put(PID_GAPS, Float.valueOf(percentage));
 
         percentage = ((float) count * 100) / nongap;
-        residueHash.put(PID_NOGAPS, new Float(percentage));
+        residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
         result[bpEnd] = residueHash;
       }
@@ -444,7 +447,8 @@ public class StructureFrequency
     int valuesCount = 0;
     rtnval[1] = 0;
     int offset = 2;
-    final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+    final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+            : 0];
     for (int c = 624; c > 0; c--)
     {
       if (vl[c] > 0)