@Override
public int getPairwiseScore(char c, char d)
{
- int pog = 0;
+ int score = 0;
try
{
: ResidueProperties.nucleotideIndex[c];
int b = (type == 0) ? ResidueProperties.aaIndex[d]
: ResidueProperties.nucleotideIndex[d];
-
- /*
- * FIXME: 2.10.1 PCA treats gap as [22] or 'X', but Tree
- * calculation treats as [23]; which is correct?
- */
- /*
- * hack to convert unassigned / unknown (including gap)
- * to index of unknown (X for amino acids, N for nucleotide)
- * TODO: statically assign gap characters to this index?
- */
-// if (type == 0)
-// {
-// if (a == ResidueProperties.maxProteinIndex)
-// {
-// a = ResidueProperties.aaIndex['X'];
-// }
-// if (b == ResidueProperties.maxProteinIndex)
-// {
-// b = ResidueProperties.aaIndex['X'];
-// }
-// }
-// if (type != 0)
-// {
-// if (a == ResidueProperties.maxNucleotideIndex)
-// {
-// a = ResidueProperties.nucleotideIndex['N'];
-// }
-// if (b == ResidueProperties.maxNucleotideIndex)
-// {
-// b = ResidueProperties.nucleotideIndex['N'];
-// }
-// }
- pog = matrix[a][b];
+ score = matrix[a][b];
} catch (Exception e)
{
// System.out.println("Unknown residue in " + A1 + " " + A2);
}
- return pog;
+ return score;
}
/**