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Searched defs:sqfp (Results 1 – 25 of 126) sorted by relevance

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/dports/biology/infernal/infernal-1.1.3/easel/
H A Desl_sqio_ascii.c529 sqascii_Close(ESL_SQFILE *sqfp) in sqascii_Close()
2025 loadmem(ESL_SQFILE *sqfp) in loadmem()
2100 loadbuf(ESL_SQFILE *sqfp) in loadbuf()
2370 skip_whitespace(ESL_SQFILE *sqfp) in skip_whitespace()
2506 config_embl(ESL_SQFILE *sqfp) in config_embl()
2728 end_embl(ESL_SQFILE *sqfp, ESL_SQ *sq) in end_embl()
2755 config_genbank(ESL_SQFILE *sqfp) in config_genbank()
2929 config_fasta(ESL_SQFILE *sqfp) in config_fasta()
3173 config_daemon(ESL_SQFILE *sqfp) in config_daemon()
3250 ESL_SQFILE sqfp; in esl_sqascii_Parse() local
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H A Desl_sqio.c99 esl_sqfile_Close(ESL_SQFILE *sqfp) in esl_sqfile_Close()
119 ESL_SQFILE *sqfp = NULL; in sqfile_open() local
1114 ESL_SQFILE *sqfp = NULL; in esl_sqfile_Cache() local
1512 ESL_SQFILE *sqfp = NULL; in main() local
1843 ESL_SQFILE *sqfp = NULL; in make_ssi_index() local
1890 ESL_SQFILE *sqfp = NULL; in utest_read() local
1926 ESL_SQFILE *sqfp = NULL; in utest_read_info() local
1974 ESL_SQFILE *sqfp = NULL; in utest_read_window() local
2054 ESL_SQFILE *sqfp = NULL; in utest_fetch_subseq() local
2151 ESL_SQFILE *sqfp; in utest_guess_mechanics() local
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H A Desl_sqio_ncbi.c566 sqncbi_Position(ESL_SQFILE *sqfp, off_t offset) in sqncbi_Position()
585 sqncbi_Close(ESL_SQFILE *sqfp) in sqncbi_Close()
706 sqncbi_IsRewindable(const ESL_SQFILE *sqfp) in sqncbi_IsRewindable()
718 sqncbi_GetError(const ESL_SQFILE *sqfp) in sqncbi_GetError()
750 sqncbi_Read(ESL_SQFILE *sqfp, ESL_SQ *sq) in sqncbi_Read()
801 sqncbi_ReadInfo(ESL_SQFILE *sqfp, ESL_SQ *sq) in sqncbi_ReadInfo()
1602 read_amino(ESL_SQFILE *sqfp, ESL_SQ *sq) in read_amino()
1654 read_dna(ESL_SQFILE *sqfp, ESL_SQ *sq) in read_dna()
2116 inmap_ncbi(ESL_SQFILE *sqfp) in inmap_ncbi()
2149 inmap_ncbi_dna(ESL_SQFILE *sqfp) in inmap_ncbi_dna()
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/dports/biology/hmmer/hmmer-3.3/easel/
H A Desl_sqio_ascii.c529 sqascii_Close(ESL_SQFILE *sqfp) in sqascii_Close()
2025 loadmem(ESL_SQFILE *sqfp) in loadmem()
2100 loadbuf(ESL_SQFILE *sqfp) in loadbuf()
2370 skip_whitespace(ESL_SQFILE *sqfp) in skip_whitespace()
2506 config_embl(ESL_SQFILE *sqfp) in config_embl()
2728 end_embl(ESL_SQFILE *sqfp, ESL_SQ *sq) in end_embl()
2755 config_genbank(ESL_SQFILE *sqfp) in config_genbank()
2929 config_fasta(ESL_SQFILE *sqfp) in config_fasta()
3173 config_daemon(ESL_SQFILE *sqfp) in config_daemon()
3250 ESL_SQFILE sqfp; in esl_sqascii_Parse() local
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H A Desl_sqio.c99 esl_sqfile_Close(ESL_SQFILE *sqfp) in esl_sqfile_Close()
119 ESL_SQFILE *sqfp = NULL; in sqfile_open() local
1114 ESL_SQFILE *sqfp = NULL; in esl_sqfile_Cache() local
1512 ESL_SQFILE *sqfp = NULL; in main() local
1843 ESL_SQFILE *sqfp = NULL; in make_ssi_index() local
1890 ESL_SQFILE *sqfp = NULL; in utest_read() local
1926 ESL_SQFILE *sqfp = NULL; in utest_read_info() local
1974 ESL_SQFILE *sqfp = NULL; in utest_read_window() local
2054 ESL_SQFILE *sqfp = NULL; in utest_fetch_subseq() local
2151 ESL_SQFILE *sqfp; in utest_guess_mechanics() local
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H A Desl_sqio_ncbi.c566 sqncbi_Position(ESL_SQFILE *sqfp, off_t offset) in sqncbi_Position()
585 sqncbi_Close(ESL_SQFILE *sqfp) in sqncbi_Close()
706 sqncbi_IsRewindable(const ESL_SQFILE *sqfp) in sqncbi_IsRewindable()
718 sqncbi_GetError(const ESL_SQFILE *sqfp) in sqncbi_GetError()
750 sqncbi_Read(ESL_SQFILE *sqfp, ESL_SQ *sq) in sqncbi_Read()
801 sqncbi_ReadInfo(ESL_SQFILE *sqfp, ESL_SQ *sq) in sqncbi_ReadInfo()
1602 read_amino(ESL_SQFILE *sqfp, ESL_SQ *sq) in read_amino()
1654 read_dna(ESL_SQFILE *sqfp, ESL_SQ *sq) in read_dna()
2116 inmap_ncbi(ESL_SQFILE *sqfp) in inmap_ncbi()
2149 inmap_ncbi_dna(ESL_SQFILE *sqfp) in inmap_ncbi_dna()
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/dports/biology/infernal/infernal-1.1.3/easel/miniapps/
H A Desl-sfetch.c100 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
213 create_ssi_index(ESL_GETOPTS *go, ESL_SQFILE *sqfp) in create_ssi_index()
292 multifetch(ESL_GETOPTS *go, FILE *ofp, char *keyfile, ESL_SQFILE *sqfp) in multifetch()
364 onefetch(ESL_GETOPTS *go, FILE *ofp, char *key, ESL_SQFILE *sqfp) in onefetch()
420 multifetch_subseq(ESL_GETOPTS *go, FILE *ofp, char *gdffile, ESL_SQFILE *sqfp) in multifetch_subseq()
458 onefetch_subseq(ESL_GETOPTS *go, FILE *ofp, ESL_SQFILE *sqfp, char *newname, char *key, uint32_t gi… in onefetch_subseq()
H A Desl-translate.c17 do_by_sequences(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_sequences()
52 do_by_windows(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_windows()
127 ESL_SQFILE *sqfp = NULL; in main() local
H A Desl-seqrange.c61 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
131 range_by_seqnum(ESL_SQFILE *sqfp, int nproc, int64_t **ret_final_sqidx) in range_by_seqnum()
H A Dcmd_downsample.c122 ESL_SQFILE *sqfp = NULL; in downsample_seqs() local
206 ESL_SQFILE *sqfp = NULL; in downsample_seqs_big() local
H A Desl-mask.c77 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
H A Desl-seqstat.c76 ESL_SQFILE *sqfp = NULL; in main() local
/dports/biology/hmmer/hmmer-3.3/easel/miniapps/
H A Desl-sfetch.c100 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
213 create_ssi_index(ESL_GETOPTS *go, ESL_SQFILE *sqfp) in create_ssi_index()
292 multifetch(ESL_GETOPTS *go, FILE *ofp, char *keyfile, ESL_SQFILE *sqfp) in multifetch()
364 onefetch(ESL_GETOPTS *go, FILE *ofp, char *key, ESL_SQFILE *sqfp) in onefetch()
420 multifetch_subseq(ESL_GETOPTS *go, FILE *ofp, char *gdffile, ESL_SQFILE *sqfp) in multifetch_subseq()
458 onefetch_subseq(ESL_GETOPTS *go, FILE *ofp, ESL_SQFILE *sqfp, char *newname, char *key, uint32_t gi… in onefetch_subseq()
H A Desl-translate.c17 do_by_sequences(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_sequences()
52 do_by_windows(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_windows()
127 ESL_SQFILE *sqfp = NULL; in main() local
H A Desl-seqrange.c61 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
131 range_by_seqnum(ESL_SQFILE *sqfp, int nproc, int64_t **ret_final_sqidx) in range_by_seqnum()
H A Dcmd_downsample.c122 ESL_SQFILE *sqfp = NULL; in downsample_seqs() local
206 ESL_SQFILE *sqfp = NULL; in downsample_seqs_big() local
H A Desl-mask.c77 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
/dports/biology/infernal/infernal-1.1.3/src/
H A Dtrcyk.c21 ESL_SQFILE *sqfp; in main() local
H A Dtruncyk_check.c41 ESL_SQFILE *sqfp; /* open seqfile for reading */ in main() local
/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dcachedb_shard.c71 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_master() local
343 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_shard() local
719 ESL_SQFILE *sqfp = NULL; in main() local
H A Dcachedb.c64 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open() local
375 ESL_SQFILE *sqfp = NULL; in main() local
H A Dgeneric_vtrace.c206 ESL_SQFILE *sqfp = NULL; in main() local
/dports/biology/hmmer/hmmer-3.3/src/
H A Dcachedb_shard.c71 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_master() local
343 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_shard() local
719 ESL_SQFILE *sqfp = NULL; in main() local
H A Dcachedb.c64 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open() local
375 ESL_SQFILE *sqfp = NULL; in main() local
H A Dgeneric_vtrace.c206 ESL_SQFILE *sqfp = NULL; in main() local

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