formatting

[jalview.git] / src / jalview / util / Comparison.java

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index f8e1fcd..9044bf9 100644 (file)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -133,19 +133,28 @@ public class Comparison
   // Another pid with region specification
   public final static float PID(String seq1, String seq2, int start, int end)
   {
-       return PID(seq1, seq2, start, end, true,false);
+    return PID(seq1, seq2, start, end, true, false);
   }
+
   /**
-   * Calculate percent identity for a pair of sequences over a particular range, with different options for ignoring gaps.
+   * Calculate percent identity for a pair of sequences over a particular range,
+   * with different options for ignoring gaps.
+   * 
    * @param seq1
    * @param seq2
-   * @param start - position in seqs
-   * @param end - position in seqs
-   * @param wcGaps - if true - gaps match any character, if false, do not match anything
-   * @param ungappedOnly - if true - only count PID over ungapped columns
+   * @param start
+   *          - position in seqs
+   * @param end
+   *          - position in seqs
+   * @param wcGaps
+   *          - if true - gaps match any character, if false, do not match
+   *          anything
+   * @param ungappedOnly
+   *          - if true - only count PID over ungapped columns
    * @return
    */
-  public final static float PID(String seq1, String seq2, int start, int end, boolean wcGaps, boolean ungappedOnly)
+  public final static float PID(String seq1, String seq2, int start,
+          int end, boolean wcGaps, boolean ungappedOnly)
   {
     int s1len = seq1.length();
     int s2len = seq2.length();
@@ -162,7 +171,7 @@ public class Comparison
       start = len - 1; // we just use a single residue for the difference
     }
 
-    int elen=len-start,bad = 0;
+    int elen = len - start, bad = 0;
     char chr1;
     char chr2;
     boolean agap;
@@ -184,24 +193,31 @@ public class Comparison
         // Faster than toUpperCase
         chr2 -= caseShift;
       }
-      
+
       if (chr1 != chr2)
       {
-       if (agap)
-       {
-               if (ungappedOnly)
-               {
-                       elen--;
-               } else if (!wcGaps) {
-                       bad++;
-               }
-       } else {
-               bad++;
-       }
+        if (agap)
+        {
+          if (ungappedOnly)
+          {
+            elen--;
+          }
+          else if (!wcGaps)
+          {
+            bad++;
+          }
+        }
+        else
+        {
+          bad++;
+        }
       }
-      
+
+    }
+    if (elen < 1)
+    {
+      return 0f;
     }
-    if (elen<1) { return 0f; }
     return ((float) 100 * (elen - bad)) / elen;
   }