X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FSimilarityParams.java;h=58b08dd7928f27b8a933a97135b6ccb6c01953d0;hb=32c56f877253fa8917d4f4640ed65d6e63376dac;hp=35e3b9cf8c27cbf47501ce3e00b5a4dea6625820;hpb=693e17575680c94d9bdc5797faa0b328bb6f7c05;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 35e3b9c..58b08dd 100644
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -1,15 +1,47 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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
 {
   /**
    * Based on Jalview's Comparison.PID method, which includes gaps and counts
    * them as matching; it counts over the length of the shorter sequence
    */
-  public static final SimilarityParamsI Jalview = new SimilarityParams(
-          true, true, true, true);
+  public static final SimilarityParamsI Jalview = new SimilarityParams(true,
+          true, true, true);
 
   /**
    * 'SeqSpace' mode PCA calculation includes gaps but does not count them as