| /dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
| H A D | kmer.cpp | 16 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in Kmer() local
18 …maxKmer = power4s[kmerSize]+1;// (int)pow(4.,k)+1; // powers of 4 everytime through. We need … in Kmer()
85 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in getKmerNumber() local
90 if(toupper(sequence[i+index]) == 'A') { kmer += (0 * power4s[kmerSize-i-1]); } in getKmerNumber()
91 else if(toupper(sequence[i+index]) == 'C') { kmer += (1 * power4s[kmerSize-i-1]); } in getKmerNumber()
92 else if(toupper(sequence[i+index]) == 'G') { kmer += (2 * power4s[kmerSize-i-1]); } in getKmerNumber()
93 else if(toupper(sequence[i+index]) == 'U') { kmer += (3 * power4s[kmerSize-i-1]); } in getKmerNumber()
94 else if(toupper(sequence[i+index]) == 'T') { kmer += (3 * power4s[kmerSize-i-1]); } in getKmerNumber()
95 else if(toupper(sequence[i+index]) == 'N') { return (int)power4s[kmerSize]; } in getKmerNumber()
118 …if(kmerNumber == power4s[kmerSize]){//pow(4.,7)){ // if the kmer number is the same as the maxKmer… in getKmerBases()
[all …]
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| H A D | sequencedb.cpp | 33 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in SequenceDB() local
35 int maxKmer = power4s[kmerSize]; in SequenceDB()
130 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in SequenceDB() local
132 int maxKmer = power4s[kmerSize]; in SequenceDB()
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| H A D | kmeralign.cpp | 17 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in KmerAlign() local
19 maxKmer = power4s[kmerSize]+1;// (int)pow(4.,k)+1; in KmerAlign()
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| H A D | kmerdb.cpp | 37 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in KmerDB() local
40 maxKmer = power4s[kmerSize]; in KmerDB()
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| /dports/biology/mothur/mothur-1.46.1/source/classifier/ |
| H A D | kmernode.cpp | 17 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in KmerNode() local
19 numPossibleKmers = power4s[kmerSize]; in KmerNode()
63 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in getKmerBases() local
67 …if(kmerNumber == power4s[kmerSize]){//pow(4.,7)){ // if the kmer number is the same as the maxKmer… in getKmerBases()
75 … int nt = (int)(kmerNumber / (float)power4s[i]) % 4; // the '%' operator returns the remainder in getKmerBases()
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| H A D | kmertree.cpp | 19 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in KmerTree() local
20 numPossibleKmers = power4s[kmerSize]; in KmerTree()
90 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in ripKmerProfile() local
102 if(toupper(sequence[j+i]) == 'A') { kmer += (0 * power4s[kmerSize-j-1]); } in ripKmerProfile()
103 else if(toupper(sequence[j+i]) == 'C') { kmer += (1 * power4s[kmerSize-j-1]); } in ripKmerProfile()
104 else if(toupper(sequence[j+i]) == 'G') { kmer += (2 * power4s[kmerSize-j-1]); } in ripKmerProfile()
105 else if(toupper(sequence[j+i]) == 'U') { kmer += (3 * power4s[kmerSize-j-1]); } in ripKmerProfile()
106 else if(toupper(sequence[j+i]) == 'T') { kmer += (3 * power4s[kmerSize-j-1]); } in ripKmerProfile()
107 else { kmer = power4s[kmerSize]; j = kmerSize; } in ripKmerProfile()
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| /dports/biology/mothur/mothur-1.46.1/source/calculators/ |
| H A D | kmerdist.cpp | 17 …int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 1677721… in KmerDist() local
20 maxKmer = power4s[kmerSize]; in KmerDist()
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