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;
}
}