/dports/biology/infernal/infernal-1.1.3/hmmer/profmark/ |
H A D | create-profmark.c | 83 struct cfg_s { struct 84 ESL_ALPHABET *abc; /* biological alphabet */ 85 ESL_RANDOMNESS *r; /* random number generator */ 86 double fragfrac; /* seqs less than x*avg length are removed from alignment */ 87 double idthresh1; /* fractional identity threshold for train/test split */ 111 static int process_dbfile (struct cfg_s *cfg, char *dbfile, int dbfmt); argument
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/dports/biology/hmmer/hmmer-3.3/profmark/ |
H A D | create-profmark.c | 83 struct cfg_s { struct 84 ESL_ALPHABET *abc; /* biological alphabet */ 85 ESL_RANDOMNESS *r; /* random number generator */ 86 double fragfrac; /* seqs less than x*avg length are removed from alignment */ 87 double idthresh1; /* fractional identity threshold for train/test split */ 111 static int process_dbfile (struct cfg_s *cfg, char *dbfile, int dbfmt); argument
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/dports/biology/infernal/infernal-1.1.3/rmark/ |
H A D | rmark-create.c | 105 struct cfg_s { struct 106 ESL_ALPHABET *abc; /* biological alphabet */ 107 ESL_RANDOMNESS *r; /* random number generator */ 108 ESL_HMM *hmm; /* HMM for generating background seqs */ 109 double fragfrac; /* seqs less than x*avg length are removed from alignment */ 110 double idthresh1; /* fractional identity threshold for train/test split */ 134 static int process_dbfile (struct cfg_s *cfg, char *dbfile, int dbfmt); argument
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | hmmsim.c | 99 struct cfg_s { struct 123 static int init_master_cfg(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
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H A D | hmmbuild.c | 161 struct cfg_s { struct 162 FILE *ofp; /* output file (default is stdout) */ 164 char *alifile; /* name of the alignment file we're building HMMs from */ 165 int fmt; /* format code for alifile */ 189 static int usual_master(const ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | nhmmscan.c | 121 struct cfg_s { struct 133 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | nhmmer.c | 204 struct cfg_s { struct 222 static int serial_master (ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | hmmsearch.c | 129 struct cfg_s { struct 141 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | phmmer.c | 137 struct cfg_s { struct 149 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | hmmscan.c | 112 struct cfg_s { struct 124 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | jackhmmer.c | 159 struct cfg_s { struct 170 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | hmmsim.c | 99 struct cfg_s { struct 123 static int init_master_cfg(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
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H A D | hmmbuild.c | 161 struct cfg_s { struct 162 FILE *ofp; /* output file (default is stdout) */ 164 char *alifile; /* name of the alignment file we're building HMMs from */ 165 int fmt; /* format code for alifile */ 189 static int usual_master(const ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | nhmmscan.c | 121 struct cfg_s { struct 133 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | nhmmer.c | 204 struct cfg_s { struct 222 static int serial_master (ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | hmmsearch.c | 129 struct cfg_s { struct 141 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | phmmer.c | 137 struct cfg_s { struct 149 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | hmmscan.c | 112 struct cfg_s { struct 124 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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H A D | jackhmmer.c | 159 struct cfg_s { struct 170 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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/dports/biology/infernal/infernal-1.1.3/src/ |
H A D | cmsim.c | 76 struct cfg_s { struct 96 static int init_cfg(const ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
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H A D | cmcalibrate.c | 111 struct cfg_s { struct 112 char *cmfile; /* name of input CM file */ 115 ESL_ALPHABET *abc; /* alphabet */ 116 ESL_STOPWATCH *w; /* stopwatch for each calibration */ 117 double *gc_freq; /* gc frequence [0..100], only used if --gc */ 119 char **namesA; /* names of all the CMs we'll calibrate */ 120 int ncm; /* what number CM we're on */ 122 char *tmpfile; /* tmp file we're writing to */ 128 int ghmm_nstates; /* number of states in the HMM */ 129 double *ghmm_sA; /* start probabilities [0..ghmm_nstates-1] */ [all …]
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H A D | cmemit.c | 70 struct cfg_s { struct 85 static int init_cfg(const ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
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H A D | cmbuild.c | 179 struct cfg_s { struct 180 FILE *ofp; /* output file (default is stdout) */ 183 int fmt; /* format code for alifile */ 184 ESL_MSAFILE *afp; /* open alifile */ 185 ESL_ALPHABET *abc; /* digital alphabet */ 191 FILE *postmsafp; /* open <postmsafile>, or NULL */ 193 float *null; /* null model */ 194 Prior_t *pri; /* mixture Dirichlet prior for the CM */ 197 fullmat_t *fullmat; /* if --rsearch, the full RIBOSUM matrix */ 200 int nali; /* which # alignment this is in file */ [all …]
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H A D | cmalign.c | 138 struct cfg_s { struct 139 char *cmfile; /* name of input CM file */ 140 char *sqfile; /* name of sequence file */ 141 CM_FILE *cmfp; /* open input CM file stream */ 142 ESL_SQFILE *sqfp; /* open sequence input file stream */ 143 ESL_ALPHABET *abc; /* alphabet for input */ 144 ESL_ALPHABET *abc_out; /* alphabet for output */ 145 int infmt; /* input alignment format */ 146 int outfmt; /* output alignment format */ 147 int be_verbose; /* TRUE if --verbose used */ [all …]
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H A D | cmsearch.c | 249 struct cfg_s { struct 262 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
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