X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FSimilarityParams.java;h=58b08dd7928f27b8a933a97135b6ccb6c01953d0;hb=4104a254062a8a225a0d9fffe3a88daf1a8c8d9a;hp=b6f2ba22fd18fb76df7bfe799f32db2ebe5dac76;hpb=e2e2b85d7a8e3d7ed6926ef1bf55eb2328e744d1;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index b6f2ba2..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
@@ -19,29 +51,47 @@ public class SimilarityParams implements SimilarityParamsI
           true, false, true, true);
 
   /**
-   * as described in the Raghava-Barton paper; considers pairwise similarity
-   * only (excludes gap-gap) and does not match gaps
+   * as described in the Raghava-Barton paper
+   * <ul>
+   * <li>ignores gap-gap</li>
+   * <li>does not score gap-residue</li>
+   * <li>includes gap-residue in lengths</li>
+   * <li>matches on longer of two sequences</li>
+   * </ul>
    */
   public static final SimilarityParamsI PID1 = new SimilarityParams(false,
           false, true, false);
 
   /**
-   * as described in the Raghava-Barton paper; considers pairwise similarity
-   * only (excludes gap-gap) and does not match gaps
+   * as described in the Raghava-Barton paper
+   * <ul>
+   * <li>ignores gap-gap</li>
+   * <li>ignores gap-residue</li>
+   * <li>matches on longer of two sequences</li>
+   * </ul>
    */
   public static final SimilarityParamsI PID2 = new SimilarityParams(false,
           false, false, false);
 
   /**
-   * as described in the Raghava-Barton paper; considers pairwise similarity
-   * only (excludes gap-gap) and does not match gaps
+   * as described in the Raghava-Barton paper
+   * <ul>
+   * <li>ignores gap-gap</li>
+   * <li>ignores gap-residue</li>
+   * <li>matches on shorter of sequences only</li>
+   * </ul>
    */
   public static final SimilarityParamsI PID3 = new SimilarityParams(false,
           false, false, true);
 
   /**
-   * as described in the Raghava-Barton paper; considers pairwise similarity
-   * only (excludes gap-gap) and does not match gaps
+   * as described in the Raghava-Barton paper
+   * <ul>
+   * <li>ignores gap-gap</li>
+   * <li>does not score gap-residue</li>
+   * <li>includes gap-residue in lengths</li>
+   * <li>matches on shorter of sequences only</li>
+   * </ul>
    */
   public static final SimilarityParamsI PID4 = new SimilarityParams(false,
           false, true, true);
@@ -50,7 +100,7 @@ public class SimilarityParams implements SimilarityParamsI
 
   private boolean matchGaps;
 
-  private boolean denominatorIncludesGaps;
+  private boolean includeGaps;
 
   private boolean denominateByShortestLength;
 
@@ -58,26 +108,26 @@ public class SimilarityParams implements SimilarityParamsI
    * Constructor
    * 
    * @param includeGapGap
-   * @param matchGap
-   * @param includeGaps
-   *          if true, gapped positions are counted in the PID denominator
+   * @param matchGapResidue
+   * @param includeGapResidue
+   *          if true, gapped positions are counted for normalisation by length
    * @param shortestLength
    *          if true, the denominator is the shorter sequence length (possibly
    *          including gaps)
    */
-  public SimilarityParams(boolean includeGapGap, boolean matchGap,
-          boolean includeGaps, boolean shortestLength)
+  public SimilarityParams(boolean includeGapGap, boolean matchGapResidue,
+          boolean includeGapResidue, boolean shortestLength)
   {
     includeGappedColumns = includeGapGap;
-    matchGaps = matchGap;
-    denominatorIncludesGaps = includeGaps;
+    matchGaps = matchGapResidue;
+    includeGaps = includeGapResidue;
     denominateByShortestLength = shortestLength;
   }
 
   @Override
-  public boolean denominatorIncludesGaps()
+  public boolean includeGaps()
   {
-    return denominatorIncludesGaps;
+    return includeGaps;
   }
 
   @Override