X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=cec9bc365e70a1db5e38cba02c246e277ac0442c;hb=e3f1e488b159029d15bbb86284667f4b482c8f69;hp=60f21c82e5fa7dc412dbd829956e578f3815c18d;hpb=bd37829796d6d9f9b8340967eea49eb0d98f70a7;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 60f21c8..cec9bc3 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -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;
   }