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// Copyright 2015 Martin C. Frith
// This class masks simple repeats (e.g. acacacacacac) in sequences,
// in one of 3 modes: normal mode, protein mode, or AT-rich DNA mode.
// The masking is insensitive to uppercase/lowercase of the input
// sequences.
// "isATrichDna" takes precedence over "isProtein".
// The "alphabet" (e.g. ACGT) is used only in normal mode.
// It is assumed that the sequences will be supplied after mapping
// letters to small integers (e.g. ACGT -> 0123). "letterToIndex"
// specifies this mapping. It is assumed that the small integers are
// less than scoreMatrixRowSize.
// "maskTable" defines how to do the masking: it maps small integers
// to masked integers.
#ifndef TANTAN_MASKER_HH
#define TANTAN_MASKER_HH
#include "ScoreMatrixRow.hh"
#include "tantan.hh"
#include <string>
namespace cbrc {
typedef unsigned char uchar;
class TantanMasker {
public:
void init(bool isProtein,
bool isATrichDna,
bool isMaskWeakRepeats,
int maxRepeatUnitLength,
const std::string &alphabet,
const uchar *letterToIndex);
void mask(uchar *seqBeg, uchar *seqEnd, const uchar *maskTable) const {
tantan::maskSequences(seqBeg, seqEnd, maxRepeatOffset, probMatrixPointers,
repeatProb, 0.05, 0.9, 0, 0, 0.5, maskTable);
}
private:
int maxRepeatOffset;
double repeatProb;
double probMatrix[scoreMatrixRowSize][scoreMatrixRowSize];
double *probMatrixPointers[scoreMatrixRowSize];
};
}
#endif
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