JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 50045dc..3a79959 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -198,9 +198,8 @@ public class AAFrequency
       if (profile)
       {
         // TODO use a 1-dimensional array with jSize, nongap in [0] and [1]
-        residueHash.put(PROFILE, new int[][]
-        { values, new int[]
-        { jSize, nongap } });
+        residueHash.put(PROFILE, new int[][] { values,
+            new int[] { jSize, nongap } });
       }
       residueHash.put(MAXCOUNT, new Integer(maxCount));
       residueHash.put(MAXRESIDUE, maxResidue);
@@ -369,8 +368,7 @@ public class AAFrequency
                 .append("%");
       }
       consensus.annotations[i] = new Annotation(maxRes,
-              mouseOver.toString(), ' ',
-              value);
+              mouseOver.toString(), ' ', value);
     }
   }
 
@@ -462,7 +460,8 @@ public class AAFrequency
    * @param hashtable
    * @return
    */
-  public static int[] extractCdnaProfile(Hashtable hashtable, boolean ignoreGaps)
+  public static int[] extractCdnaProfile(Hashtable hashtable,
+          boolean ignoreGaps)
   {
     // this holds #seqs, #ungapped, and then codon count, indexed by encoded
     // codon triplet
@@ -507,7 +506,7 @@ public class AAFrequency
     result[1] = distinctValuesCount;
     return Arrays.copyOfRange(result, 0, j);
   }
-    
+
   /**
    * Compute a consensus for the cDNA coding for a protein alignment.
    * 
@@ -664,8 +663,7 @@ public class AAFrequency
         final int pct = codonCount * 100 / totalCount;
         String codon = String
                 .valueOf(CodingUtils.decodeCodon(codonEncoded));
-        percent = fmt == null ? Integer.toString(pct) : fmt
-                .form(pct);
+        percent = fmt == null ? Integer.toString(pct) : fmt.form(pct);
         if (showProfileLogo || codonCount == modalCodonCount)
         {
           if (percent.equals(lastPercent) && j > 0)
@@ -678,8 +676,7 @@ public class AAFrequency
             if (samePercent.length() > 0)
             {
               mouseOver.append(samePercent).append(": ")
-                      .append(lastPercent)
-                      .append("% ");
+                      .append(lastPercent).append("% ");
             }
             samePercent.setLength(0);
             samePercent.append(codon);