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
{
/**