X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=546a2144bd0934404ed7378d0c4bbefcf234632a;hb=83a7efc57926ebf046f95de5291eb439563eb953;hp=7b0858d502d70a7a5aac3582478afcc6cea7f1e0;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 7b0858d..546a214 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);
       }
@@ -217,7 +218,8 @@ public class StructureFrequency
       {
         if (canonicalOrWobblePairCount >= otherPairCount)
         {
-          maxResidue = (canonicalOrWobblePairCount - canonical) < canonical ? "("
+          maxResidue = (canonicalOrWobblePairCount - canonical) < canonical
+                  ? "("
                   : "[";
         }
         else
@@ -252,8 +254,9 @@ 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);
         }
@@ -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)
@@ -464,23 +468,4 @@ public class StructureFrequency
     System.arraycopy(rtnval, 0, result, 1, rtnval.length);
     return result;
   }
-
-  public static void main(String args[])
-  {
-    // Short test to see if checkBpType works
-    ArrayList<String> test = new ArrayList<String>();
-    test.add("A");
-    test.add("c");
-    test.add("g");
-    test.add("T");
-    test.add("U");
-    for (String i : test)
-    {
-      for (String j : test)
-      {
-        System.out.println(i + "-" + j + ": "
-                + Rna.isCanonicalOrWobblePair(i.charAt(0), j.charAt(0)));
-      }
-    }
-  }
 }