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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 .
+ * 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
+ *
+ *
+ * Quantification of the variation in percentage identity for protein sequence alignments
+ * Raghava, GP and Barton, GJ
+ * BMC Bioinformatics. 2006 Sep 19;7:415
+ *
+ *
+ * @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
+ *
+ * - ignores gap-gap
+ * - does not score gap-residue
+ * - includes gap-residue in lengths
+ * - matches on longer of two sequences
+ *
+ */
+ public static final SimilarityParamsI PID1 = new SimilarityParams(false,
+ false, true, false);
+
+ /**
+ * as described in the Raghava-Barton paper
+ *
+ * - ignores gap-gap
+ * - ignores gap-residue
+ * - matches on longer of two sequences
+ *
+ */
+ public static final SimilarityParamsI PID2 = new SimilarityParams(false,
+ false, false, false);
+
+ /**
+ * as described in the Raghava-Barton paper
+ *
+ * - ignores gap-gap
+ * - ignores gap-residue
+ * - matches on shorter of sequences only
+ *
+ */
+ public static final SimilarityParamsI PID3 = new SimilarityParams(false,
+ false, false, true);
+
+ /**
+ * as described in the Raghava-Barton paper
+ *
+ * - ignores gap-gap
+ * - does not score gap-residue
+ * - includes gap-residue in lengths
+ * - matches on shorter of sequences only
+ *
+ */
+ 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;
+ }
+}