public class ScoreMatrix implements SimilarityScoreModelI,
PairwiseScoreModelI
{
+ private static final char GAP_CHARACTER = Comparison.GAP_DASH;
+
/*
* an arbitrary score to assign for identity of an unknown symbol
* (this is the value on the diagonal in the * column of the NCBI matrix)
private static final int UNKNOWN_IDENTITY_SCORE = 1;
/*
- * this fields records which gap character (if any) is used in the alphabet;
- * space, dash or dot are recognised as gap symbols
- */
- private char gapCharacter = '0';
-
- /*
* Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
* for pairwise scoring; 2.10.2 uses gap score (last column) in
* score matrix (JAL-2397)
short pos = 0;
for (char c : alphabet)
{
- if (Comparison.isGap(c))
- {
- gapCharacter = c;
- }
-
if (c <= MAX_ASCII)
{
index[c] = pos;
}
/**
- * Answers the matrix index for the gap character, or -1 if unmapped in the
- * matrix. Use this method only if using <code>getMatrix</code> in order to
- * compute scores directly (without symbol lookup) for efficiency.
- *
- * @return
- * @see #getMatrix()
- */
- public int getGapIndex()
- {
- return getMatrixIndex(gapCharacter);
- }
-
- /**
* Returns the pairwise score for substituting c with d. If either c or d is
* an unexpected character, returns 1 for identity (c == d), else the minimum
* score value in the matrix.
SimilarityParamsI options)
{
char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X')
- : gapCharacter;
+ : GAP_CHARACTER;
String[] seqs = seqstrings.getSequenceStrings(gapChar);
return findSimilarities(seqs, options);
}
}
}
- char c1 = i >= len1 ? gapCharacter : seq1.charAt(i);
- char c2 = i >= len2 ? gapCharacter : seq2.charAt(i);
+ char c1 = i >= len1 ? GAP_CHARACTER : seq1.charAt(i);
+ char c2 = i >= len2 ? GAP_CHARACTER : seq2.charAt(i);
boolean gap1 = Comparison.isGap(c1);
boolean gap2 = Comparison.isGap(c2);