X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=b681aa6a34362f0504ac66cf0bcc82cfd8526796;hb=63cead20b09743e899a22cb89f1c09e4d41cc8c0;hp=a4ba204187f82fb9430a73e04abd7bcd627f2afc;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index a4ba204..b681aa6 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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)