From 9d701bbe1b456aac498c5665cb3d7ac00a58db57 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 30 May 2005 16:33:29 +0000
Subject: [PATCH] comments

---
 src/jalview/util/Comparison.java |   16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 0366430..03abd0c 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -8,6 +8,14 @@ public class Comparison {
   {
     return Comparison.compare(ii,jj,0,ii.getLength()-1);
   }
+  /**
+   * this was supposed to be an ungapped pid calculation
+   * @param ii SequenceI
+   * @param jj SequenceI
+   * @param start int
+   * @param end int
+   * @return float
+   */
   public static float compare(SequenceI ii, SequenceI jj, int start, int end) {
 
      String si   = ii.getSequence();
@@ -52,7 +60,13 @@ public class Comparison {
     return pid;
   }
 
-  /**    */
+  /**
+   * this is a gapped PID calculation
+   *
+   * @param s1 SequenceI
+   * @param s2 SequenceI
+   * @return float
+   */
   public static float PID(SequenceI s1 , SequenceI s2)
   {
     int len;
-- 
1.7.10.2