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Searched defs:cfg_s (Results 1 – 25 of 28) sorted by relevance

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/dports/biology/infernal/infernal-1.1.3/hmmer/profmark/
H A Dcreate-profmark.c83 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
/dports/biology/hmmer/hmmer-3.3/profmark/
H A Dcreate-profmark.c83 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
/dports/biology/infernal/infernal-1.1.3/rmark/
H A Drmark-create.c105 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
/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dhmmsim.c99 struct cfg_s { struct
123 static int init_master_cfg(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
H A Dhmmbuild.c161 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
H A Dnhmmscan.c121 struct cfg_s { struct
133 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dnhmmer.c204 struct cfg_s { struct
222 static int serial_master (ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dhmmsearch.c129 struct cfg_s { struct
141 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dphmmer.c137 struct cfg_s { struct
149 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dhmmscan.c112 struct cfg_s { struct
124 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Djackhmmer.c159 struct cfg_s { struct
170 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
/dports/biology/hmmer/hmmer-3.3/src/
H A Dhmmsim.c99 struct cfg_s { struct
123 static int init_master_cfg(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
H A Dhmmbuild.c161 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
H A Dnhmmscan.c121 struct cfg_s { struct
133 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dnhmmer.c204 struct cfg_s { struct
222 static int serial_master (ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dhmmsearch.c129 struct cfg_s { struct
141 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dphmmer.c137 struct cfg_s { struct
149 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Dhmmscan.c112 struct cfg_s { struct
124 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
H A Djackhmmer.c159 struct cfg_s { struct
170 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument
/dports/biology/infernal/infernal-1.1.3/src/
H A Dcmsim.c76 struct cfg_s { struct
96 static int init_cfg(const ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
H A Dcmcalibrate.c111 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 …]
H A Dcmemit.c70 struct cfg_s { struct
85 static int init_cfg(const ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf); argument
H A Dcmbuild.c179 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 …]
H A Dcmalign.c138 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 …]
H A Dcmsearch.c249 struct cfg_s { struct
262 static int serial_master(ESL_GETOPTS *go, struct cfg_s *cfg); argument

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