/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 356 && numBases<BASELIMIT;) { in fread_alf() 380 read->base[numBases] = ch; in fread_alf() 381 read->prob_A[numBases] = 0; in fread_alf() 382 read->prob_C[numBases] = 0; in fread_alf() 383 read->prob_G[numBases] = 0; in fread_alf() 384 read->prob_T[numBases] = 0; in fread_alf() 385 read->basePos[numBases] = bp; in fread_alf() 386 ++numBases; in fread_alf() 389 read->base[numBases] = 0; in fread_alf() [all …]
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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 71 LONG_INTPARAMETER("numBases", &numBases) in execute() 83 ((end == UNSPECIFIED_INT) && (numBases == UNSPECIFIED_INT))) in execute() 90 if((end != UNSPECIFIED_INT) && (numBases != UNSPECIFIED_INT)) in execute() 97 else if(numBases != UNSPECIFIED_INT) in execute() 99 end = start + numBases; in execute()
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/dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
H A D | sffread.cpp | 75 numBases = be_int4(*(unsigned int *)(readNumBases)); in readSff() 135 flowIndex.resize(numBases); in readSff() 136 char* flowI = new char[numBases]; in readSff() 138 for (int i = 0; i < numBases; i++) { in readSff() 147 char* readBases = new char[numBases]; in readSff() 148 in.read(&(*readBases), numBases); in readSff() 153 qualScores.resize(numBases, 0); in readSff() 154 char* scores = new char[numBases]; in readSff() 156 for (int i = 0; i < numBases; i++) { in readSff() 284 out.write(entireRead[11], numBases); //write bases in printSff() [all …]
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H A D | sequence.cpp | 71 …if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the… in Sequence() 475 numBases = 0; in initialize() 505 numBases = unaligned.length(); in setUnaligned() 605 return numBases; in getNumBases() 648 for(int j=0;j<numBases;j++){ in getAmbigBases() 676 for(int j=1;j<numBases;j++){ in getLongHomoPolymer() 750 if (alignmentLength != numBases) { isAligned = true; } in getEndPos() 760 if(!isAligned){ endPos = numBases; } in getEndPos() 795 for(int i=numBases-1;i>=0;i--){ in reverseComplement() 811 if(numBases > length){ in trim() [all …]
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H A D | sffread.hpp | 84 unsigned int getNumBases() { return numBases; } in getNumBases() 102 void setNumBases(unsigned int n) { numBases = n; } in setNumBases() 117 unsigned int numBases; member in SffRead
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H A D | protein.cpp | 439 numBases = 0; in initialize() 461 numBases = unaligned.size(); in setUnaligned() 539 int Protein::getNumBases(){ return numBases; } in getNumBases() 623 if (alignmentLength != numBases) { isAligned = true; } in getEndPos() 633 if(!isAligned){ endPos = numBases; } in getEndPos() 666 if(numBases > length){ in trim() 668 numBases = length; in trim()
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H A D | optiblastmatrix.cpp | 61 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq; in readBlast() local 76 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in readBlast() 80 lengthThisSeq = numBases; in readBlast() 114 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in readBlast() 185 lengthThisSeq = numBases; in readBlast() 290 …in >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuer… in readBlast() 294 lengthThisSeq = numBases; in readBlast() 340 …in >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuer… in readBlast() 424 lengthThisSeq = numBases; in readBlast()
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H A D | optidb.cpp | 21 numBases = baseMap.size(); //A,T,G,C,-,N in OptiDB() 45 thisDistribution.resize(numBases); in get() 253 counts.resize(numBases, 0.0); in calcIndicatorColumns()
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H A D | optidb.hpp | 42 int alignedLength, numBases; member in OptiDB
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | abiview.c | 101 ajlong numBases; in main() local 142 numBases = ajSeqABIGetNBase(fp); in main() 148 numBases = base_end; in main() 150 if(numBases < base_start) in main() 152 base_start,numBases); in main() 156 window = (ajint) numBases+1; /* Lossy cast */ in main() 182 ajSeqABIReadSeq(fp,baseO,numBases,&nseq); in main() 225 while(nstart < numBases-1) in main() 227 if(nstop > numBases) in main() 228 nstop = (ajint) numBases; /* Lossy cast */ in main() [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/ |
H A D | ABIFormat.cpp | 473 uint numPoints, numBases; in loadABIObjects() local 509 numBases = 0; in loadABIObjects() 517 cd.prob_A.resize(numBases + 1); in loadABIObjects() 518 cd.prob_C.resize(numBases + 1); in loadABIObjects() 519 cd.prob_G.resize(numBases + 1); in loadABIObjects() 520 cd.prob_T.resize(numBases + 1); in loadABIObjects() 521 cd.baseCalls.resize(numBases + 1); in loadABIObjects() 602 QVector<uchar> conf(numBases); in loadABIObjects() 615 QByteArray qualCodes(numBases, 0); in loadABIObjects() 747 if (numBases > 1) { in loadABIObjects() [all …]
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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 197 numResidues = numBases = 0; in checkDNAFlag() 208 numBases++; in checkDNAFlag() 215 numBases++; in checkDNAFlag() 222 if ((numBases == 0) || (numResidues == 0)) in checkDNAFlag() 226 ratio = (float)numBases / (float)numResidues; in checkDNAFlag()
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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() argument 131 for (i=0;i<(ajint)numBases;i++) in ajSeqABIReadConfid() 157 AjBool ajSeqABIReadSeq(AjPFile fp,ajlong baseO,ajlong numBases, in ajSeqABIReadSeq() argument 163 ajDebug("ajSeqABIReadSeq base0 %Ld numBases %Ld\n", baseO, numBases); in ajSeqABIReadSeq() 167 for (i=0;i<(ajint)numBases;i++) in ajSeqABIReadSeq() 265 ajlong numBases; in ajSeqABIGetNBase() local 271 if(!seqABIGetFlag(fp,BASEtag,2,3,&numBases)) in ajSeqABIGetNBase() 272 if(!seqABIGetFlag(fp,BASEtag,1,3,&numBases)) in ajSeqABIGetNBase() 278 return (ajint) numBases; in ajSeqABIGetNBase() 337 void ajSeqABIGetBasePosition(AjPFile fp,ajlong numBases, in ajSeqABIGetBasePosition() argument [all …]
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H A D | ajseqabi.h | 73 void ajSeqABIGetBasePosition(AjPFile fp,ajlong numBases, 90 AjBool ajSeqABIReadConfid(AjPFile fp,ajlong pconO,ajlong numBases, 92 AjBool ajSeqABIReadSeq(AjPFile fp,ajlong baseO,ajlong numBases,
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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 132 resize(numBases, n, 0); in resizeToReadLength() 158 numBases[i] += 1; in registerRead() 166 if (numBases[i] == 0u || minScores[i] > qual) in registerRead() 168 if (numBases[i] == 0u || maxScores[i] < qual) in registerRead() 180 meanScores[i] = (1.0 * sumScores[i]) / numBases[i]; in finalizeStats() 188 unsigned n = numBases[i]; // Number of bases. in finalizeStats() 331 << stats.numBases[i] << "\t" in main()
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/dports/biology/checkm/CheckM-1.0.18/checkm/ |
H A D | binUnion.py | 50 def numBases(self): member in UnionBin 138 fiftyPercent = 0.5 * current.numBases() 142 fiftyPercentBest = 0.5 * bestBin.numBases() 163 … bestBin.numBases(), 164 … current.numBases(),
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/dports/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/ |
H A D | Assembly.pm | 378 $self->{totalbp} = defined $all->{numBases} ? $all->{numBases} : 0; 379 $self->{totalbp1k} = defined $large->{numBases} ? $large->{numBases} : 0; 446 $out{numBases} = $avglen;
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/dports/biology/mothur/mothur-1.46.1/source/calculators/ |
H A D | kimura.cpp | 15 int numBases = A.getAlignLength(); in calcDist() local 21 for (int i = 0; i < numBases; i++) { in calcDist()
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/dports/biology/bbmap/bbmap/current/dna/ |
H A D | MotifMulti.java | 57 public int numBases() { in numBases() method in MotifMulti 58 return sub[0].numBases(); in numBases()
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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 67 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in read() 71 lengthThisSeq = numBases; in read() 102 …fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >>… in read() 175 lengthThisSeq = numBases; in read()
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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() argument 562 fill_n(base_count, numBases, 0); in CollectNucleotideFrequences() 636 void CAlnVec::CollectProteinFrequences(const string& col, int base_count[], int numBases) in CollectProteinFrequences() argument 640 fill_n(base_count, numBases, 0); in CollectProteinFrequences() 646 if (0<=pos && pos < numBases) in CollectProteinFrequences() 655 const int numBases = isNucleotide ? 4 : 26; in CreateConsensus() local 698 CollectNucleotideFrequences(segs[i], base_count, numBases); in CreateConsensus() 700 CollectProteinFrequences(segs[i], base_count, numBases); in CreateConsensus() 711 for (int k = 0; k < numBases; ++k) { in CreateConsensus()
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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() argument 562 fill_n(base_count, numBases, 0); in CollectNucleotideFrequences() 636 void CAlnVec::CollectProteinFrequences(const string& col, int base_count[], int numBases) in CollectProteinFrequences() argument 640 fill_n(base_count, numBases, 0); in CollectProteinFrequences() 646 if (0<=pos && pos < numBases) in CollectProteinFrequences() 655 const int numBases = isNucleotide ? 4 : 26; in CreateConsensus() local 698 CollectNucleotideFrequences(segs[i], base_count, numBases); in CreateConsensus() 700 CollectProteinFrequences(segs[i], base_count, numBases); in CreateConsensus() 711 for (int k = 0; k < numBases; ++k) { in CreateConsensus()
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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 165 numBases++; in minCoverageFilter() 173 int coverage = ((numCovered/(float)numBases)*100); in minCoverageFilter() 545 float numBases = (countA + countB) /(float) 2; in computePercentID() local 547 if (numBases == 0) { return 0; } in computePercentID() 549 float percentIdentical = (numIdentical/(float)numBases) * 100; in computePercentID()
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/dports/games/osgg/Osgg-32d9e02/ |
H A D | server.cpp | 108 int numBases; // Number of bases on map, set by loadMap member 296 gameInfo.numBases=0; in loadMap() 385 gameInfo.numBases++; in loadMap() 393 if(te.type==entBase && te.id != gameInfo.numBases) in loadMap() 395 …cout << "error: base entity have id:" << te.id << " but numBases is:" << gameInfo.numBases << endl; in loadMap() 933 if(gameInfo.numBases > 1) in main()
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/dports/java/bouncycastle15/crypto-169/core/src/test/java/org/bouncycastle/math/test/ |
H A D | PrimesTest.java | 158 private static boolean referenceIsMRProbablePrime(BigInteger x, int numBases) 162 for (int i = 0; i < numBases; ++i)
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