/dports/biology/infernal/infernal-1.1.3/easel/ |
H A D | esl_sqio_ascii.c | 529 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 [all …]
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H A D | esl_sqio.c | 99 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 [all …]
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H A D | esl_sqio_ncbi.c | 566 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() [all …]
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/dports/biology/hmmer/hmmer-3.3/easel/ |
H A D | esl_sqio_ascii.c | 529 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 [all …]
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H A D | esl_sqio.c | 99 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 [all …]
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H A D | esl_sqio_ncbi.c | 566 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() [all …]
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/dports/biology/infernal/infernal-1.1.3/easel/miniapps/ |
H A D | esl-sfetch.c | 100 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()
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H A D | esl-translate.c | 17 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
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H A D | esl-seqrange.c | 61 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()
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H A D | cmd_downsample.c | 122 ESL_SQFILE *sqfp = NULL; in downsample_seqs() local 206 ESL_SQFILE *sqfp = NULL; in downsample_seqs_big() local
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H A D | esl-mask.c | 77 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
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H A D | esl-seqstat.c | 76 ESL_SQFILE *sqfp = NULL; in main() local
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/dports/biology/hmmer/hmmer-3.3/easel/miniapps/ |
H A D | esl-sfetch.c | 100 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()
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H A D | esl-translate.c | 17 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
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H A D | esl-seqrange.c | 61 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()
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H A D | cmd_downsample.c | 122 ESL_SQFILE *sqfp = NULL; in downsample_seqs() local 206 ESL_SQFILE *sqfp = NULL; in downsample_seqs_big() local
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H A D | esl-mask.c | 77 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
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/dports/biology/infernal/infernal-1.1.3/src/ |
H A D | trcyk.c | 21 ESL_SQFILE *sqfp; in main() local
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H A D | truncyk_check.c | 41 ESL_SQFILE *sqfp; /* open seqfile for reading */ in main() local
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | cachedb_shard.c | 71 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
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H A D | cachedb.c | 64 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open() local 375 ESL_SQFILE *sqfp = NULL; in main() local
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H A D | generic_vtrace.c | 206 ESL_SQFILE *sqfp = NULL; in main() local
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/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | cachedb_shard.c | 71 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
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H A D | cachedb.c | 64 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open() local 375 ESL_SQFILE *sqfp = NULL; in main() local
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H A D | generic_vtrace.c | 206 ESL_SQFILE *sqfp = NULL; in main() local
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