+/*
+ * 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
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);
private boolean matchGaps;
- private boolean denominatorIncludesGaps;
+ private boolean includeGaps;
private boolean denominateByShortestLength;
* 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
{
return matchGaps;
}
+
+ /**
+ * IDE-generated hashCode method
+ */
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + (denominateByShortestLength ? 1231 : 1237);
+ result = prime * result + (includeGappedColumns ? 1231 : 1237);
+ result = prime * result + (includeGaps ? 1231 : 1237);
+ result = prime * result + (matchGaps ? 1231 : 1237);
+ return result;
+ }
+
+ /**
+ * IDE-generated equals method
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ SimilarityParams other = (SimilarityParams) obj;
+ if (denominateByShortestLength != other.denominateByShortestLength)
+ {
+ return false;
+ }
+ if (includeGappedColumns != other.includeGappedColumns)
+ {
+ return false;
+ }
+ if (includeGaps != other.includeGaps)
+ {
+ return false;
+ }
+ if (matchGaps != other.matchGaps)
+ {
+ return false;
+ }
+ return true;
+ }
}