From 15e5ce4fe2019ff41fcab75395e9280d952145a8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 23 Mar 2017 16:10:21 +0000
Subject: [PATCH] JAL-838 class javadoc added

---
 src/jalview/analysis/scoremodels/SimilarityParams.java |   12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 35e3b9c..e5751ca 100644
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -2,6 +2,18 @@ package jalview.analysis.scoremodels;
 
 import jalview.api.analysis.SimilarityParamsI;
 
+/**
+ * A class to hold parameters that configure the pairwise similarity
+ * calculation. Based on the paper
+ * 
+ * <pre>
+ * Quantification of the variation in percentage identity for protein sequence alignments
+ * Raghava, GP and Barton, GJ
+ * BMC Bioinformatics. 2006 Sep 19;7:415
+ * </pre>
+ * 
+ * @see https://www.ncbi.nlm.nih.gov/pubmed/16984632
+ */
 public class SimilarityParams implements SimilarityParamsI
 {
   /**
-- 
1.7.10.2