Merge branch 'develop' into trial_merge/JAL-1950

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

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
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+/*
+ * 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);
+
+  /**
+   * '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);
+
+  private boolean includeGappedColumns;
+
+  private boolean matchGaps;
+
+  private boolean includeGaps;
+
+  private boolean denominateByShortestLength;
+
+  /**
+   * Constructor
+   * 
+   * @param includeGapGap
+   * @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 matchGapResidue,
+          boolean includeGapResidue, boolean shortestLength)
+  {
+    includeGappedColumns = includeGapGap;
+    matchGaps = matchGapResidue;
+    includeGaps = includeGapResidue;
+    denominateByShortestLength = shortestLength;
+  }
+
+  @Override
+  public boolean includeGaps()
+  {
+    return includeGaps;
+  }
+
+  @Override
+  public boolean denominateByShortestLength()
+  {
+    return denominateByShortestLength;
+  }
+
+  @Override
+  public boolean includeGappedColumns()
+  {
+    return includeGappedColumns;
+  }
+
+  @Override
+  public boolean matchGaps()
+  {
+    return matchGaps;
+  }
+}