| /dports/biology/mothur/mothur-1.46.1/source/calculators/ |
| H A D | kimura.cpp | 15 int numBases = A.getAlignLength(); in calcDist() local
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| /dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
| H A D | protein.hpp | 88 int numBases; member in Protein
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| H A D | sequence.hpp | 100 int numBases; member in Sequence
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| H A D | optidb.hpp | 42 int alignedLength, numBases; member in OptiDB
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| H A D | sffread.hpp | 117 unsigned int numBases; member in SffRead
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| H A D | blastdb.cpp | 201 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, searchScore; in findClosestMegaBlast() local
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajseqabi.c | 121 AjBool ajSeqABIReadConfid(AjPFile fp,ajlong pconO,ajlong numBases, in ajSeqABIReadConfid()
157 AjBool ajSeqABIReadSeq(AjPFile fp,ajlong baseO,ajlong numBases, in ajSeqABIReadSeq()
265 ajlong numBases; in ajSeqABIGetNBase() local
337 void ajSeqABIGetBasePosition(AjPFile fp,ajlong numBases, in ajSeqABIGetBasePosition()
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| /dports/biology/bamutil/bamUtil-1.0.15/src/ |
| H A D | ReadReference.cpp | 60 int numBases = UNSPECIFIED_INT; in execute() local
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| /dports/biology/bbmap/bbmap/current/dna/ |
| H A D | MotifMulti.java | 57 public int numBases() { in numBases() method in MotifMulti
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| H A D | MotifSimple.java | 84 public int numBases() { in numBases() method in MotifSimple
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| H A D | MotifProbsN.java | 250 public int numBases() { in numBases() method in MotifProbsN
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| H A D | Motif.java | 200 public abstract int numBases(); in numBases() method in Motif
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| /dports/biology/clustalw/clustalw-2.1/src/alignment/ |
| H A D | Sequence.cpp | 193 int c, numResidues, numBases; in checkDNAFlag() local
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| /dports/biology/canu/canu-2.2/src/bogart/ |
| H A D | AS_BAT_ReadInfo.H | 39 uint64 numBases(void) { return(_numBases); }; in numBases() function
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| /dports/biology/checkm/CheckM-1.0.18/checkm/ |
| H A D | binUnion.py | 50 def numBases(self): member in UnionBin
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| /dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
| H A D | seqIOALF.c | 348 int numBases; /* number of nucleotides read in */ in fread_alf() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/ |
| H A D | alnvec.cpp | 558 void CAlnVec::CollectNucleotideFrequences(const string& col, int base_count[], int numBases) in CollectNucleotideFrequences()
636 void CAlnVec::CollectProteinFrequences(const string& col, int base_count[], int numBases) in CollectProteinFrequences()
655 const int numBases = isNucleotide ? 4 : 26; in CreateConsensus() local
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/ |
| H A D | alnvec.cpp | 558 void CAlnVec::CollectNucleotideFrequences(const string& col, int base_count[], int numBases) in CollectNucleotideFrequences()
636 void CAlnVec::CollectProteinFrequences(const string& col, int base_count[], int numBases) in CollectProteinFrequences()
655 const int numBases = isNucleotide ? 4 : 26; in CreateConsensus() local
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| /dports/biology/mothur/mothur-1.46.1/source/chimera/ |
| H A D | maligner.cpp | 158 int numBases = 0; in minCoverageFilter() local
545 float numBases = (countA + countB) /(float) 2; in computePercentID() local
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| /dports/biology/mothur/mothur-1.46.1/source/read/ |
| H A D | readblast.cpp | 49 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq; in read() local
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| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | MultiStateAligner9PacBioAdapter3.java | 1271 public static final int maxQuality(int numBases){ in maxQuality()
1279 public static final int maxImperfectScore(int numBases){ in maxImperfectScore()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/fx_tools/ |
| H A D | fx_fastq_stats.cpp | 83 seqan::String<int64_t> numBases; member
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | abiview.c | 101 ajlong numBases; in main() local
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| /dports/devel/pyside2/pyside-setup-opensource-src-5.15.2/sources/shiboken2/libshiboken/ |
| H A D | bindingmanager.cpp | 239 int numBases = ((d && d->is_multicpp) ? getNumberOfCppBaseClasses(Py_TYPE(sbkObj)) : 1); in releaseWrapper() local
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| /dports/devel/pyside2-tools/pyside-setup-opensource-src-5.15.2/sources/shiboken2/libshiboken/ |
| H A D | bindingmanager.cpp | 239 int numBases = ((d && d->is_multicpp) ? getNumberOfCppBaseClasses(Py_TYPE(sbkObj)) : 1); in releaseWrapper() local
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