Merge branch 'develop' into features/JAL-2393customMatrices

[jalview.git] / src / jalview / analysis / scoremodels / SimilarityParams.java

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 8b6b7d0..e5751ca 100644 (file)
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -2,20 +2,77 @@ 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);
 
+  /**
+   * 'SeqSpace' mode PCA calculation includes gaps but does not count them as
+   * matching; it uses the longest sequence length
+   */
+  public static final SimilarityParamsI SeqSpace = new SimilarityParams(
+          true, false, true, true);
+
+  /**
+   * 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
+   * <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
+   * <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
+   * <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);
 
@@ -23,7 +80,7 @@ public class SimilarityParams implements SimilarityParamsI
 
   private boolean matchGaps;
 
-  private boolean denominatorIncludesGaps;
+  private boolean includeGaps;
 
   private boolean denominateByShortestLength;
 
@@ -31,26 +88,26 @@ 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)
    */
-  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