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Squashed 'lib/mmseqs/' changes from ddc19be5..7f5c0003
7f5c0003 Fix memory issue b80ce103 Fix issues in masksequence a2d01d01 Rework masking and add N repeat masking e3b16faf Fix issue soedinglab/MMseqs2#916 git-subtree-dir: lib/mmseqs git-subtree-split: 7f5c0003a9135add5a2b6f14ab822e527b3df547
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,136 @@ | ||
| #include "Masker.h" | ||
| #include <algorithm> // for std::toupper | ||
|
|
||
| Masker::Masker(BaseMatrix &s) : subMat(s), probMatrix(s) | ||
| { | ||
| maxSeqLen = 1; | ||
| charSequence = (unsigned char *)malloc(maxSeqLen * sizeof(char)); | ||
| maskLetterNum = subMat.aa2num[(int)'X']; | ||
| } | ||
|
|
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| Masker::~Masker() { | ||
| free(charSequence); | ||
| } | ||
|
|
||
| int Masker::maskSequence(Sequence & seq, bool maskTantan, double maskProb, | ||
| bool maskLowerCaseLetter, int maskNrepeats) { | ||
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| int maskedResidues = 0; | ||
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| if(maskTantan){ | ||
| // 1. Apply tantan masking without influencing by repeat mask | ||
| maskedResidues += tantan::maskSequences(seq.numSequence, | ||
| seq.numSequence + seq.L, | ||
| 50 /*maxCycleLength*/, | ||
| probMatrix.probMatrixPointers, | ||
| 0.005 /*repeatProb*/, | ||
| 0.05 /*repeatEndProb*/, | ||
| 0.9 /*repeatOffsetProbDecay*/, | ||
| 0, 0, | ||
| maskProb /*minMaskProb*/, | ||
| probMatrix.hardMaskTable); | ||
| } | ||
| if( maskNrepeats > 0){ | ||
| // 2. Generate the mask for repeats | ||
| maskedResidues += maskRepeats(seq.numSequence, seq.L, maskNrepeats, maskLetterNum); | ||
| } | ||
| // 3. Handle lowercase masking | ||
| if(maskLowerCaseLetter){ | ||
| if ((Parameters::isEqualDbtype(seq.getSequenceType(), Parameters::DBTYPE_AMINO_ACIDS) || | ||
| Parameters::isEqualDbtype(seq.getSequenceType(), Parameters::DBTYPE_NUCLEOTIDES))) { | ||
| const char *charSeq = seq.getSeqData(); | ||
| for (int i = 0; i < seq.L; i++) { | ||
| if (std::islower((unsigned char)charSeq[i])) { | ||
| seq.numSequence[i] = maskLetterNum; // Apply masking | ||
| maskedResidues++; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| // 4. Finalize masking | ||
| if(maskTantan || maskNrepeats || maskLowerCaseLetter){ | ||
| finalizeMasking(seq.numSequence, seq.L); | ||
| } | ||
| return maskedResidues; | ||
| } | ||
|
|
||
| void Masker::maskPssm(Sequence& centerSequence, float maskProb, PSSMCalculator::Profile& pssmRes) { | ||
| if ((size_t)centerSequence.L > maxSeqLen) { | ||
| maxSeqLen = sizeof(char) * centerSequence.L * 1.5; | ||
| charSequence = (unsigned char*)realloc(charSequence, maxSeqLen); | ||
| } | ||
| memcpy(charSequence, centerSequence.numSequence, sizeof(unsigned char) * centerSequence.L); | ||
| tantan::maskSequences(charSequence, charSequence + centerSequence.L, | ||
| 50 /*options.maxCycleLength*/, | ||
| probMatrix.probMatrixPointers, | ||
| 0.005 /*options.repeatProb*/, | ||
| 0.05 /*options.repeatEndProb*/, | ||
| 0.9 /*options.repeatOffsetProbDecay*/, | ||
| 0, 0, | ||
| maskProb /*options.minMaskProb*/, | ||
| probMatrix.hardMaskTable); | ||
|
|
||
| for (int pos = 0; pos < centerSequence.L; pos++) { | ||
| if (charSequence[pos] == maskLetterNum) { | ||
| for (size_t aa = 0; aa < Sequence::PROFILE_AA_SIZE; aa++) { | ||
| pssmRes.pssm[pos * Sequence::PROFILE_AA_SIZE + aa] = -1; | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
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|
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| int Masker::maskRepeats(unsigned char * numSequence, const unsigned int seqLen, int maskNrepeating, char maskChar) { | ||
|
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| unsigned int repeatCount = 0; | ||
| int startOfRepeat = -1; | ||
| char previousChar = '\0'; | ||
| int maskedResidues = 0; // Counter for masked residues | ||
|
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||
| for (unsigned int pos = 0; pos < seqLen; ++pos) { | ||
| char currentChar = numSequence[pos]; | ||
|
|
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| if (currentChar == previousChar) { | ||
| repeatCount++; | ||
| } else { | ||
| if (repeatCount > (unsigned int)maskNrepeating) { | ||
| for (unsigned int i = startOfRepeat; i < pos; ++i) { | ||
| numSequence[i] = maskChar; | ||
| maskedResidues++; | ||
| } | ||
| } | ||
| repeatCount = 1; | ||
| startOfRepeat = pos; | ||
| previousChar = currentChar; | ||
| } | ||
| } | ||
|
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| // Handle the last run | ||
| if (repeatCount > (unsigned int)maskNrepeating) { | ||
| for (unsigned int i = startOfRepeat; i < seqLen; ++i) { | ||
| numSequence[i] = maskChar; | ||
| maskedResidues++; | ||
| } | ||
| } | ||
|
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| return maskedResidues; | ||
| } | ||
|
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| void Masker::finalizeMasking(unsigned char * numSequence, const unsigned int seqLen) { | ||
| unsigned char maskChar = probMatrix.hardMaskTable[0]; | ||
|
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| for (unsigned int i = 0; i < seqLen; i++) { | ||
| unsigned char code = numSequence[i]; | ||
| numSequence[i] = (code == maskChar || code == maskLetterNum) ? maskLetterNum : numSequence[i]; | ||
| } | ||
| } | ||
|
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| void Masker::applySoftmasking(unsigned char *charSequence, const unsigned char * num_sequence, unsigned int seqLen) { | ||
| for (unsigned int pos = 0; pos < seqLen; pos++) { | ||
| // If masked, lowercase (soft) or uppercase (hard) could be applied here if needed. | ||
| // For simplicity, we treat maskChar as masked and others as uppercase: | ||
| charSequence[pos] = (num_sequence[pos] == maskLetterNum) | ||
| ? (char)std::tolower(charSequence[pos]) | ||
| : (char)std::toupper(charSequence[pos]); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| #ifndef MMSEQS_MASKER_H | ||
| #define MMSEQS_MASKER_H | ||
|
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| #include "Parameters.h" | ||
| #include "Sequence.h" | ||
| #include "SubstitutionMatrix.h" | ||
| #include "tantan.h" | ||
| #include "PSSMCalculator.h" | ||
| #include <cctype> | ||
|
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| class Masker { | ||
| public: | ||
| Masker(BaseMatrix &subMat); | ||
|
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| ~Masker(); | ||
|
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| int maskSequence(Sequence & seq, bool maskTantan, double maskProb, | ||
| bool maskLowerCaseLetter, int maskNrepeating); | ||
|
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| void maskPssm(Sequence& centerSequence, float maskProb, PSSMCalculator::Profile& pssmRes); | ||
|
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| void applySoftmasking(unsigned char *charSequence, const unsigned char * numSequence, unsigned int seqLen); | ||
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| char maskLetterNum; | ||
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| private: | ||
| int maskRepeats(unsigned char *numSequence, const unsigned int seqLen, int maskNrepeating, char maskChar); | ||
|
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| void finalizeMasking(unsigned char * numSequence, const unsigned int seqLen); | ||
|
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| BaseMatrix &subMat; | ||
| ProbabilityMatrix probMatrix; | ||
|
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| unsigned char * charSequence; | ||
| size_t maxSeqLen; | ||
| }; | ||
| #endif |
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