| /dports/audio/julius/julius-4.1.2/gramtools/nextword/ |
| H A D | wtoken.c | 26 put_wtoken(WTOKEN **wseq, int nseq) in put_wtoken()
69 int nseq; in new_get_wtoken() local
141 free_wtoken(WTOKEN **wseq, int nseq) in free_wtoken()
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/hmmer2/ |
| H A D | weight.cpp | 45 GSCWeights(char **aseq, int nseq, int alen, float *wgt) in GSCWeights()
95 upweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, int node) in upweight()
109 downweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, float *fwt, int node) in downweight()
153 VoronoiWeights(char **aseq, int nseq, int alen, float *wgt) in VoronoiWeights()
393 BlosumWeights(char **aseqs, int nseq, int alen, float maxid, float *wgt) in BlosumWeights()
462 PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt) in PositionBasedWeights()
699 SingleLinkCluster(char **aseq, int nseq, int alen, float maxid, in SingleLinkCluster()
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| H A D | checksum.cpp | 54 GCGMultchecksum(char **seqs, int nseq) in GCGMultchecksum()
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| /dports/biology/clustal-omega/clustal-omega-1.2.4/src/squid/ |
| H A D | weight.c | 43 GSCWeights(char **aseq, int nseq, int alen, float *wgt) in GSCWeights()
93 upweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, int node) in upweight()
107 downweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, float *fwt, int node) in downweight()
151 VoronoiWeights(char **aseq, int nseq, int alen, float *wgt) in VoronoiWeights()
391 BlosumWeights(char **aseqs, int nseq, int alen, float maxid, float *wgt) in BlosumWeights()
460 PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt) in PositionBasedWeights()
701 SingleLinkCluster(char **aseq, int nseq, int alen, float maxid, in SingleLinkCluster()
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| H A D | alignio.c | 40 AllocAlignment(int nseq, int alen, char ***ret_aseq, AINFO *ainfo) in AllocAlignment()
141 SAMizeAlignment(char **aseq, int nseq, int alen) in SAMizeAlignment()
187 SAMizeAlignmentByGapFrac(char **aseq, int nseq, int alen, float maxgap) in SAMizeAlignmentByGapFrac()
511 RandomAlignment(char **rseqs, SQINFO *sqinfo, int nseq, float pop, float pex, in RandomAlignment()
632 AlignmentHomogenousGapsym(char **aseq, int nseq, int alen, char gapsym) in AlignmentHomogenousGapsym()
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| /dports/biology/tRNAscan-SE/tRNAscan-SE-2.0/src/ |
| H A D | maxmodelmaker.c | 333 int nseq, in init_maxmx()
439 int nseq, in recurse_maxmx()
956 int nseq, in transpose_alignment()
1012 int nseq, in singlet_emissions()
1093 int nseq, in pair_emissioncost()
1186 int nseq, in frommatp_transtable()
1269 int nseq, in frommatl_transtable()
1336 int nseq, in frommatr_transtable()
1402 int nseq, in frombeginr_transtable()
1462 int nseq, in frombeginl_transtable()
[all …]
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| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | constants.c | 66 static void calcfreq_nuc( int nseq, char **seq, double *datafreq ) in calcfreq_nuc()
106 static void calcfreq( int nseq, char **seq, double *datafreq ) in calcfreq()
140 static void calcfreq_extended( int nseq, char **seq, double *datafreq ) in calcfreq_extended()
201 void constants( int nseq, char **seq ) in constants()
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| H A D | f2cl.c | 21 void setmark_clustal( int nlen, int nseq, char **seq, char *mark ) in setmark_clustal()
135 void setmark( int nlen, int nseq, char **seq, char *mark ) in setmark()
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | tranalign.c | 46 AjPSeq nseq; /* next nucleic sequence to align */ in main() local
214 const AjPSeq nseq, const AjPSeq pseq, in tranalign_AddGaps()
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| H A D | coderet.c | 253 AjPSeq nseq = NULL; in coderet_put_seq() local
300 AjPSeq nseq = NULL; in coderet_put_rest() local
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| H A D | fuzzpro.c | 42 ajuint nseq = 0; in main() local
|
| /dports/math/octave-forge-dataframe/dataframe-1.2.0/inst/@dataframe/ |
| H A D | ndims.m | 8 nseq = max(cellfun(@length, df.x_rep)); variable
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| H A D | subsref.m | 376 nseq = 1; variable
379 nseq = max (cellfun (@length, df.x_rep(indc))); variable
385 nseq = max (cellfun (@length, df.x_rep(indc))); variable
389 nseq = length (inds); variable
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| /dports/biology/wise/wise2.4.1/src/HMMer2/ |
| H A D | weight.c | 90 upweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, int node) in upweight()
104 downweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, float *fwt, int node) in downweight()
456 FilterAlignment(char **aseq, int nseq, AINFO *ainfo, float cutoff, in FilterAlignment()
540 SampleAlignment(char **aseq, int nseq, AINFO *ainfo, int sample, in SampleAlignment()
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| /dports/biology/infernal/infernal-1.1.3/easel/miniapps/ |
| H A D | esl-alistat.c | 72 int nseq; /* number of sequences in the msa */ in main() local
605 …LPHABET *abc, double **abc_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, ch… in dump_infocontent_info()
675 …LPHABET *abc, double **abc_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, ch… in dump_residue_info()
722 …info(FILE *fp, double **pp_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, ch… in dump_posterior_column_info()
871 double nseq; in dump_insert_info() local
962 …double **abc_ct, int no_ambig, int use_weights, int nali, int64_t alen, int nseq, char *msa_name, … in dump_column_residue_counts()
1016 …SA *msa, ESL_ALPHABET *abc, double ***bp_ct, int use_weights, int nali, int nseq, char *msa_name, … in dump_basepair_counts()
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| /dports/biology/hmmer/hmmer-3.3/easel/miniapps/ |
| H A D | esl-alistat.c | 72 int nseq; /* number of sequences in the msa */ in main() local
605 …LPHABET *abc, double **abc_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, ch… in dump_infocontent_info()
675 …LPHABET *abc, double **abc_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, ch… in dump_residue_info()
722 …info(FILE *fp, double **pp_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, ch… in dump_posterior_column_info()
871 double nseq; in dump_insert_info() local
962 …double **abc_ct, int no_ambig, int use_weights, int nali, int64_t alen, int nseq, char *msa_name, … in dump_column_residue_counts()
1016 …SA *msa, ESL_ALPHABET *abc, double ***bp_ct, int use_weights, int nali, int nseq, char *msa_name, … in dump_basepair_counts()
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/qhop/ |
| H A D | qhop_setup_tj.F | 1 subroutine qhop_setup(mparms,nparms,matm,natm,mseq,nseq, argument
26 integer matm,natm,mseq,nseq,nparms,mparms local
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| /dports/biology/jalview/jalview/src/jalview/workers/ |
| H A D | ConsensusThread.java | 226 long nseq = getSequences().length; in deriveConsensus() local
244 long nseq = getSequences().length; in deriveGap() local
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| /dports/biology/jalview/jalview/src/jalview/controller/ |
| H A D | AlignViewController.java | 175 int nseq = findColumnsWithFeature(featureType, sqcol, bs); in markColumnsContainingFeatures() local
242 int nseq = 0; in findColumnsWithFeature() local
429 int nseq = viewport.getSearchResults().markColumns(sqcol, bs); in markHighlightedColumns() local
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| /dports/comms/hamlib/hamlib-4.3.1/rigs/yaesu/ |
| H A D | yaesu.h | 42 unsigned char nseq[YAESU_CMD_LENGTH]; /* native cmd sequence */ member
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| /dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
| H A D | ratemeyerhaeseler.cpp | 158 int nseq = phylo_tree->leafNum; in initializeRates() local
318 int nseq = phylo_tree->leafNum; in optimizeRates() local
407 int nseq = phylo_tree->leafNum; in computeFunction() local
421 int nseq = phylo_tree->leafNum; in computeFuncDerv() local
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| /dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_guidetree.h | 80 TSize nseq = (TSize) std::sqrt((double)length(mat)); in njTree() local
338 TSize nseq, in _upgmaTreeMerge()
368 TSize nseq, in _upgmaTreeMerge()
394 TSize nseq, in _upgmaTreeMerge()
419 TSize nseq, in _upgmaTreeMerge()
593 TSize nseq = (TSize) std::sqrt((double)length(mat)); in upgmaTree() local
712 TSize nseq = numVertices(pairGraph); in upgmaTree() local
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/qhop/ |
| H A D | qhop_setup_tj.F | 1 subroutine qhop_setup(mparms,nparms,matm,natm,mseq,nseq, argument
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| /dports/net-im/p5-Net-XMPP2/Net-XMPP2-0.14/lib/Net/XMPP2/ |
| H A D | Parser.pm | 125 sub nseq { subroutine
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| /dports/science/InsightToolkit/ITK-5.0.1/Modules/ThirdParty/HDF5/src/itkhdf5/src/ |
| H A D | H5Dscatgath.c | 104 size_t nseq; /* Number of sequences generated */ in H5D__scatter_file() local
205 size_t nseq; /* Number of sequences generated */ in H5D__gather_file() local
299 size_t nseq; /* Number of sequences generated */ in H5D__scatter_mem() local
387 size_t nseq; /* Number of sequences generated */ in H5D__gather_mem() local
814 size_t nseq; /* Number of sequences generated */ in H5D__compound_opt_read() local
|