| /dports/biology/mmseqs2/MMseqs2-13-45111/src/commons/ |
| H A D | Sequence.cpp | 169 …nce::parseSpacedPattern(unsigned int kmerSize, bool spaced, const std::string& spacedKmerPattern) { in parseSpacedPattern() argument
172 char* pattern = new char[spacedKmerPattern.size()]; in parseSpacedPattern()
173 for (size_t i = 0; i < spacedKmerPattern.size(); ++i) { in parseSpacedPattern()
174 switch (spacedKmerPattern[i]) { in parseSpacedPattern()
196 …return std::make_pair<const char *, unsigned int>((const char *) pattern, spacedKmerPattern.size()… in parseSpacedPattern()
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| H A D | Sequence.h | 447 …> parseSpacedPattern(unsigned int kmerSize, bool spaced, const std::string& spacedKmerPattern);
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| H A D | Parameters.h | 383 std::string spacedKmerPattern; // User-specified kmer pattern variable
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| H A D | Parameters.cpp | 63 …ser-specified spaced k-mer pattern", typeid(std::string), (void *) &spacedKmerPattern, "^1[01]*1$"… in Parameters()
2065 spacedKmerPattern = ""; in setDefaults()
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| /dports/biology/mmseqs2/MMseqs2-13-45111/src/util/ |
| H A D | indexdb.cpp | 37 if (par.spacedKmerPattern != PrefilteringIndexReader::getSpacedPattern(&index)) in findIncompatibleParameter()
134 … par.spacedKmer, par.spacedKmerPattern, par.compBiasCorrection, in indexdb()
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| H A D | alignbykmer.cpp | 168 …maxSeqLen, querySeqType, subMat, par.kmerSize, par.spacedKmer, false, true, par.spacedKmerPattern); in alignbykmer()
169 …axSeqLen, targetSeqType, subMat, par.kmerSize, par.spacedKmer, false, true, par.spacedKmerPattern); in alignbykmer()
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| /dports/biology/mmseqs2/MMseqs2-13-45111/src/prefiltering/ |
| H A D | PrefilteringIndexReader.cpp | 54 … bool hasSpacedKmer, const std::string &spacedKmerPattern, in createIndexFile() argument
111 if (spacedKmerPattern.empty() != false) { in createIndexFile()
113 …writer.writeData(spacedKmerPattern.c_str(), spacedKmerPattern.length(), SPACEDPATTERN, SPLIT_META); in createIndexFile()
191 …(maxSeqLen, seqType, subMat, kmerSize, hasSpacedKmer, compBiasCorrection, true, spacedKmerPattern); in createIndexFile()
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| H A D | PrefilteringIndexReader.h | 59 … BaseMatrix *seedSubMat, int maxSeqLen, bool spacedKmer, const std::string &spacedKmerPattern,
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| H A D | Prefiltering.h | 72 std::string spacedKmerPattern; variable
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| H A D | Prefiltering.cpp | 34 spacedKmerPattern(par.spacedKmerPattern), in Prefiltering()
156 spacedKmerPattern = PrefilteringIndexReader::getSpacedPattern(tidxdbr); in Prefiltering()
509 …eqLen, targetSeqType, kmerSubMat, kmerSize, spacedKmer, aaBiasCorrection, true, spacedKmerPattern); in getIndexTable()
777 …qLen(), querySeqType, kmerSubMat, kmerSize, spacedKmer, aaBiasCorrection, true, spacedKmerPattern); in runSplit()
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| /dports/biology/mmseqs2/MMseqs2-13-45111/src/linclust/ |
| H A D | kmerindexdb.cpp | 221 if (par.spacedKmerPattern.empty() != false) { in kmerindexdb()
223 …dbw.writeData(par.spacedKmerPattern.c_str(), par.spacedKmerPattern.length(), PrefilteringIndexRead… in kmerindexdb()
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| H A D | LinsearchIndexReader.cpp | 275 if (par.spacedKmerPattern != PrefilteringIndexReader::getSpacedPattern(&index)) in findIncompatibleParameter()
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| H A D | kmermatcher.cpp | 100 …eqLen, querySeqType, subMat, adjustedKmerSize, par.spacedKmer, false, true, par.spacedKmerPattern); in fillKmerPositionArray()
1187 parameters.spacedKmerPattern = ""; in setKmerLengthAndAlphabet()
1205 parameters.spacedKmerPattern = ""; in setKmerLengthAndAlphabet()
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