/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | distmat.c | 57 ajint nseqs); 84 ajint nseqs; in main() local 155 if(nseqs<2) in main() 275 for(j=0;j<nseqs;++j) in distmat_Tamura() 292 for(j=0; j<nseqs; j++) in distmat_Tamura() 520 ajint nseqs) in distmat_KimuraProt() argument 643 for(j=0;j<nseqs;++j) in distmat_calc_match() 808 for(j=0;j<nseqs;++j) in distmat_TajimaNei() 821 for(j=0;j<nseqs;j++) in distmat_TajimaNei() 1064 for(i=0;i<nseqs;i++) in distmat_JinNei() [all …]
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H A D | cons.c | 47 ajint nseqs; in main() local 72 nseqs = ajSeqsetGetSize(seqset); in main() 73 if(nseqs<2) in main() 74 ajFatal("Insufficient sequences (%d) to create a matrix",nseqs); in main() 77 for(i=0;i<nseqs;++i) /* check sequences are same length */ in main() 91 embConsCalc (seqset, cmpmatrix, nseqs, mlen, in main()
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H A D | consambig.c | 47 ajint nseqs; in main() local 63 nseqs = ajSeqsetGetSize(seqset); in main() 64 if(nseqs<2) in main() 65 ajFatal("Insufficient sequences (%d) to create a matrix",nseqs); in main() 68 for(i=0;i<nseqs;++i) /* check sequences are same length */ in main()
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H A D | sizeseq.c | 39 ajuint nseqs; in main() local 50 nseqs = ajSeqsetGetSize(seqset); in main() 54 for(i=nseqs; i>0; i--) in main() 59 for(i=0; i<nseqs; i++) in main()
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H A D | aligncopypair.c | 46 ajuint nseqs; in main() local 60 nseqs = ajSeqsetGetSize(seqset); in main() 70 imax = nseqs-1; in main() 73 for(j=i+1;j<nseqs;j++) in main()
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H A D | prophecy.c | 137 ajuint nseqs; in prophecy_simple_matrix() local 151 nseqs = ajSeqsetGetSize(seqset); in prophecy_simple_matrix() 152 if(nseqs<2) in prophecy_simple_matrix() 158 for(i=0;i<nseqs;++i) in prophecy_simple_matrix() 169 for(i=0;i<nseqs;++i) in prophecy_simple_matrix() 261 ajuint nseqs; in prophecy_gribskov_profile() local 304 for(j=0;j<nseqs;++j) in prophecy_gribskov_profile() 358 for(j=0;j<nseqs;++j) in prophecy_gribskov_profile() 495 ajuint nseqs; in prophecy_henikoff_profile() local 535 for(j=0;j<nseqs;++j) in prophecy_henikoff_profile() [all …]
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/dports/biology/clustal-omega/clustal-omega-1.2.4/src/clustal/ |
H A D | seq.c | 102 msa = MSAAlloc(prMSeq->nseqs, in AliStat() 268 assert(i<prMSeq->nseqs && j<prMSeq->nseqs); in SeqSwap() 503 if (0 == prMSeq->nseqs) { in ReadSequences() 543 prMSeq->sqinfo[prMSeq->nseqs].name, prMSeq->sqinfo[prMSeq->nseqs].len, in ReadSequences() 551 prMSeq->nseqs++; in ReadSequences() 718 (*prMSeq)->nseqs = 0; in NewMSeq() 751 (*prMSeqDest_p)->nseqs = prMSeqSrc->nseqs; in CopyMSeq() 857 (*mseq)->nseqs = 0; in FreeMSeq() 1124 if (1 == prMSeq->nseqs) { in SeqsAreAligned() 1255 (*prMSeqDest_p)->nseqs++; in AddSeq() [all …]
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H A D | mbed.c | 322 assert(iNumSeeds>0 && iNumSeeds<=prMSeq->nseqs); in SeqToVec() 379 0, iNumSeeds, 0, prMSeq->nseqs, in SeqToVec() 493 iNumSeeds, prMSeq->nseqs); in SeedSelection() 511 iNumSeeds, prMSeq->nseqs); in SeedSelection() 1202 iNumSeeds = (int) NUMBER_OF_SEEDS(prMSeq->nseqs); in Mbed() 1203 if (iNumSeeds >= prMSeq->nseqs) { in Mbed() 1205 iNumSeeds = prMSeq->nseqs-1; in Mbed() 1221 for (iI=0; iI<prMSeq->nseqs; iI++) { in Mbed() 1440 prSubClusterMSeq->nseqs = iNSeqInCluster; in Mbed() 1483 0, prSubClusterMSeq->nseqs, 0, prSubClusterMSeq->nseqs, in Mbed() [all …]
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H A D | hhalign_wrapper.c | 108 for (iS = 0; iS < mseq->nseqs; iS++){ in SanitiseUnknown() 163 for (iS = 0; iS < mseq->nseqs; iS++){ in TranslateUnknown2Ambiguity() 281 assert(prMSeq->nseqs > iProfProfSeparator); in ReAttachLeadingGaps() 284 iSize2 = prMSeq->nseqs - iProfProfSeparator; in ReAttachLeadingGaps() 310 for (i = 0; i < prMSeq->nseqs; i++){ in ReAttachLeadingGaps() 509 int iNseq = prMSeq->nseqs; /* number of sequences */ in PosteriorProbabilities() 658 for (iI = 0; iI < prMSeq->nseqs; iI++){ in PileUp() 671 for (iI = 1; iI < MIN(prMSeq->nseqs, iClustersize); iI++){ in PileUp() 700 while (iI < prMSeq->nseqs){ in PileUp() 986 int iSizeProf2 = prMSeq->nseqs - iProfProfSeparator; in HHalignWrapper() [all …]
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/dports/biology/hhsuite/hh-suite-3.3.0/src/cs/ |
H A D | alignment-inl.h | 37 Resize(nseqs, ncols); in Alignment() 38 for (size_t k = 0; k < nseqs; ++k) in Alignment() 65 const size_t nseqs = seqs.size(); in Init() local 446 if (nseqs == 0 || ncols == 0) in Resize() 450 seqs_.Resize(ncols, nseqs); in Resize() 454 headers_.resize(nseqs); in Resize() 611 Vector<int> mapping(nseqs()); in Rearrange() 699 const size_t nseqs = ali.nseqs(); in GlobalWeightsAndDiversity() local 739 Normalize(&wg[0], nseqs); in GlobalWeightsAndDiversity() 778 const size_t nseqs = ali.nseqs(); in PositionSpecificWeightsAndDiversity() local [all …]
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/dports/biology/mothur/mothur-1.46.1/source/read/ |
H A D | readphylip.cpp | 36 int square, nseqs; square = 0; in read() local 44 else { convert(numTest, nseqs); } in read() 49 list = new ListVector(nseqs); in read() 74 DMatrix->resize(nseqs); in read() 80 for(int i=1;i<nseqs;i++){ in read() 131 int index = nseqs; in read() 133 for(int i=1;i<nseqs;i++){ in read() 236 DMatrix->resize(nseqs); in read() 242 for(int i=1;i<nseqs;i++){ in read() 302 int index = nseqs; in read() [all …]
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H A D | readcluster.cpp | 94 list = new ListVector(nseqs); in convertPhylip2Column() 108 for(int i=0;i<nseqs;i++){ in convertPhylip2Column() 121 for(int i=1;i<nseqs;i++){ in convertPhylip2Column() 163 for(int i=1;i<nseqs;i++){ in convertPhylip2Column() 170 for(int j=0;j<nseqs;j++){ in convertPhylip2Column() 185 for(int j=0;j<nseqs;j++){ in convertPhylip2Column() 261 int square, nseqs; in convertPhylip2Column() local 286 for(int i=0;i<nseqs;i++){ in convertPhylip2Column() 299 for(int i=1;i<nseqs;i++){ in convertPhylip2Column() 340 for(int i=1;i<nseqs;i++){ in convertPhylip2Column() [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/nucleus/ |
H A D | embcons.c | 63 ajint nseqs, ajint mlen,float fplural,float setcase, in embConsCalc() argument 94 AJCNEW(seqcharptr,nseqs); in embConsCalc() 105 for(i=0;i<nseqs;i++) /* get sequence as string */ in embConsCalc() 118 for(i=0;i<nseqs;i++) in embConsCalc() 121 for(i=0;i<nseqs;i++) /* generate score for columns */ in embConsCalc() 128 for(j=i+1;j<nseqs;j++) in embConsCalc() 150 for(i=0;i<nseqs;i++) in embConsCalc() 164 for(j=0;j<nseqs;j++) in embConsCalc() 188 for(i=0;i<nseqs;i++) in embConsCalc() 196 for(i=0;i<nseqs;i++) in embConsCalc() [all …]
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/dports/biology/mothur/mothur-1.46.1/source/ |
H A D | clusterclassic.cpp | 54 list = new ListVector(nseqs); in readPhylipFile() 63 dMatrix.resize(nseqs); in readPhylipFile() 72 for(int i=0;i<nseqs;i++){ in readPhylipFile() 90 for(int i=1;i<nseqs;i++){ in readPhylipFile() 149 int index = nseqs; in readPhylipFile() 151 for(int i=1;i<nseqs;i++){ in readPhylipFile() 157 for(int j=0;j<nseqs;j++){ in readPhylipFile() 245 dMatrix.resize(nseqs); in readPhylipFile() 330 int index = nseqs; in readPhylipFile() 417 for(int i=1;i<nseqs;i++){ in getSmallCell() [all …]
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H A D | venn.cpp | 61 if (nseqs) { in getPic() 126 if (nseqs) { in getPic() 186 if (nseqs) { in getPic() 275 if (nseqs) { in getPic() 444 if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal); } in getPic() 566 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); } in getPic() 573 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); } in getPic() 580 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); } in getPic() 818 if (nseqs) { in getPic() 879 if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); } in getPic() [all …]
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/dports/biology/vt/vt-0.57721/ |
H A D | profile_chrom.cpp | 219 int32_t nseqs; in print_pdf() local 220 const char** seq_names = bcf_hdr_seqnames(odr->hdr, &nseqs); in print_pdf() 221 int32_t* len = bcf_hdr_seqlen(odr->hdr, &nseqs); in print_pdf() 223 for (int32_t i=0; i<nseqs; ++i) in print_pdf() 240 if(nseqs) free(seq_names); in print_pdf() 241 if(nseqs) free(len); in print_pdf() 280 int32_t nseqs; in print_stats() local 284 int32_t* len = bcf_hdr_seqlen(odr->hdr, &nseqs); in print_stats() 287 for (int32_t i=0; i<nseqs; ++i) in print_stats() 305 if(nseqs) free(seq_names); in print_stats() [all …]
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H A D | bcf_synced_reader.cpp | 114 int32_t nseqs; in BCFSyncedReader() local 115 const char ** seqnames = bcf_hdr_seqnames(hdrs[i], &nseqs); in BCFSyncedReader() 117 if (nseqs0==0 || nseqs==0 || nseqs0!=nseqs) in BCFSyncedReader() 123 for (size_t j=0; j<nseqs; ++j) in BCFSyncedReader() 151 int32_t nseqs = 0; in add_interval() local 156 seq_names = bcf_hdr_seqnames(hdrs[i], &nseqs); in add_interval() 157 for (size_t j=0; j<nseqs; ++j) in add_interval() 171 seq_names = tbx_seqnames(tbxs[i], &nseqs); in add_interval() 172 for (size_t j=0; j<nseqs; ++j) in add_interval()
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/dports/biology/emboss/EMBOSS-6.6.0/jemboss/org/emboss/jemboss/editor/ |
H A D | Consensus.java | 126 int nseqs = seqs.size(); in calculateCons() local 138 float score[] = new float[nseqs]; in calculateCons() 158 for(i=0;i<nseqs;i++) in calculateCons() 161 for(i=0;i<nseqs;i++) /* generate score for columns */ in calculateCons() 168 for(j=i+1;j<nseqs;j++) in calculateCons() 184 for(i=0;i<nseqs;i++) in calculateCons() 197 for(i=0;i<nseqs;i++) /* find +ve matches in the column */ in calculateCons() 215 for(j=0;j<nseqs;j++) in calculateCons() 231 for(i=0;i<nseqs;i++) in calculateCons() 243 for(i=0;i<nseqs;i++) in calculateCons() [all …]
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/dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
H A D | optimatrix.cpp | 35 long long nseqs; in readPhylip() local 49 else { convert(numTest, nseqs); } in readPhylip() 58 vector<bool> singleton; singleton.resize(nseqs, true); in readPhylip() 62 for(long long i=1;i<nseqs;i++){ in readPhylip() 80 for(long long i=1;i<nseqs;i++){ in readPhylip() 85 for(long long j=0;j<nseqs;j++){ in readPhylip() 123 in >> nseqs >> name; in readPhylip() 133 for(long long i=1;i<nseqs;i++){ in readPhylip() 158 long long index = nseqs; in readPhylip() 162 for(long long i=1;i<nseqs;i++){ in readPhylip() [all …]
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/dports/biology/tRNAscan-SE/tRNAscan-SE-2.0/src/ |
H A D | seqstat_main.c | 40 int nseqs; in main() local 95 nseqs = 0; in main() 106 nseqs++; in main() 112 printf("Number of sequences: %d\n", nseqs); in main() 116 printf("Average length: %.1f\n", (float) total / (float) nseqs); in main()
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/dports/biology/emboss/EMBOSS-6.6.0/jemboss/org/emboss/jemboss/gui/form/ |
H A D | ListFilePanel.java | 119 int nseqs = 0; in getArrayListFile() local 123 nseqs++; in getArrayListFile() 126 String list[] = new String[nseqs]; in getArrayListFile() 172 int nseqs = 0; in getSequence() local 177 nseqs++; in getSequence() 178 if(nseqs == n) in getSequence()
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/dports/biology/jalview/jalview/test/jalview/io/ |
H A D | NewickFileTests.java | 127 Vector<SequenceNode> oseqs, nseqs; in testTreeIO() local 137 nseqs = new TreeModel(new SequenceI[0], null, nf_regen) in testTreeIO() 141 nseqs.size() > 0); in testTreeIO() 142 SequenceI[] nsqs = new SequenceI[nseqs.size()]; in testTreeIO() 143 for (int i = 0, iSize = nseqs.size(); i < iSize; i++) in testTreeIO() 145 nsqs[i] = (SequenceI) nseqs.get(i).element(); in testTreeIO() 157 for (int i = 0, iSize = nseqs.size(); i < iSize; i++) in testTreeIO()
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/dports/biology/mothur/mothur-1.46.1/source/commands/ |
H A D | removedistscommand.cpp | 186 int square, nseqs; in readPhylip() local 196 else { convert(numTest, nseqs); } in readPhylip() 209 for(int i=0;i<nseqs;i++){ in readPhylip() 222 for(int i=1;i<nseqs;i++){ in readPhylip() 234 for(int i=1;i<nseqs;i++){ in readPhylip() 238 for(int j=0;j<nseqs;j++){ in readPhylip() 257 out << (nseqs-names.size()) << endl; in readPhylip() 262 for(int i=0;i<nseqs;i++){ in readPhylip() 281 for(int i=0;i<nseqs;i++){ in readPhylip() 289 for(int j=0;j<nseqs;j++){ in readPhylip() [all …]
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H A D | getdistscommand.cpp | 185 int square, nseqs; square = 0; in readPhylip() local 195 else { convert(numTest, nseqs); } in readPhylip() 207 for(int i=0;i<nseqs;i++){ in readPhylip() 220 for(int i=1;i<nseqs;i++){ in readPhylip() 232 for(int i=1;i<nseqs;i++){ in readPhylip() 236 for(int j=0;j<nseqs;j++){ in readPhylip() 259 for(int i=0;i<nseqs;i++){ in readPhylip() 278 for(int i=0;i<nseqs;i++){ in readPhylip() 286 for(int j=0;j<nseqs;j++){ in readPhylip() 311 in3 >> nseqs; util.gobble(in3); in readPhylip()
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/dports/biology/mothur/mothur-1.46.1/source/clearcut/ |
H A D | fasta.cpp | 309 long int bufsize, nseqs = NJ_INITIAL_NSEQS; in NJ_read_fasta() local 431 if(seq == nseqs) { in NJ_read_fasta() 435 nseqs *= 2; in NJ_read_fasta() 437 alignment->titles = (char **)realloc(alignment->titles, nseqs*sizeof(char *)); in NJ_read_fasta() 443 alignment->data = (char *)realloc(alignment->data, alignment->length*nseqs*sizeof(char)); in NJ_read_fasta() 488 nseqs = NJ_INITIAL_NSEQS; in NJ_read_fasta() 489 alignment->data = (char *)calloc(alignment->length*nseqs, sizeof(char)); in NJ_read_fasta()
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