X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=17d3a7013b7b3f7de10ff6ff17268ede7f957bd0;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=22e1ab7b39d3070c163f3bcd4dbcfb9b6d1e40f5;hpb=b0f76adef2787dd14566525e66a4073278e75d67;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 22e1ab7..17d3a70 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -40,8 +40,9 @@ public class Comparison
 
   public static final char GAP_DASH = '-';
 
-  public static final String GapChars = new String(new char[] { GAP_SPACE,
-      GAP_DOT, GAP_DASH });
+  public static final String GapChars = new String(
+          new char[]
+          { GAP_SPACE, GAP_DOT, GAP_DASH });
 
   /**
    * DOCUMENT ME!
@@ -71,7 +72,8 @@ public class Comparison
    *          int
    * @return float
    */
-  public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+  public static float compare(SequenceI ii, SequenceI jj, int start,
+          int end)
   {
     String si = ii.getSequenceAsString();
     String sj = jj.getSequenceAsString();
@@ -97,8 +99,8 @@ public class Comparison
     {
       for (int j = 0; j < jlen; j++)
       {
-        if (si.substring(start + j, start + j + 1).equals(
-                sj.substring(start + j, start + j + 1)))
+        if (si.substring(start + j, start + j + 1)
+                .equals(sj.substring(start + j, start + j + 1)))
         {
           match++;
         }
@@ -112,8 +114,8 @@ public class Comparison
     {
       for (int j = 0; j < jlen; j++)
       {
-        if (si.substring(start + j, start + j + 1).equals(
-                sj.substring(start + j, start + j + 1)))
+        if (si.substring(start + j, start + j + 1)
+                .equals(sj.substring(start + j, start + j + 1)))
         {
           match++;
         }
@@ -150,7 +152,8 @@ public class Comparison
    * @deprecated use PIDModel.computePID()
    */
   @Deprecated
-  public final static float PID(String seq1, String seq2, int start, int end)
+  public final static float PID(String seq1, String seq2, int start,
+          int end)
   {
     return PID(seq1, seq2, start, end, true, false);
   }
@@ -419,8 +422,8 @@ public class Comparison
         flattened.add(s);
       }
     }
-    final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
-            .size()]);
+    final SequenceI[] oneDArray = flattened
+            .toArray(new SequenceI[flattened.size()]);
     return isNucleotide(oneDArray);
   }