| /dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
| H A D | fm_alphabet.c | 35 if ( meta->alph_type == fm_DNA) { in fm_alphabetCreate()
43 } else if ( meta->alph_type == fm_AMINO) { in fm_alphabetCreate()
53 if ( meta->alph_type == fm_DNA /*|| meta->alph_type == fm_DNA_full*/) in fm_alphabetCreate()
59 if ( meta->alph_type == fm_DNA) { in fm_alphabetCreate()
86 } else if ( meta->alph_type == fm_AMINO) { in fm_alphabetCreate()
97 …if ( (meta->alph_type == fm_DNA /*|| meta->alph_type == fm_DNA_full*/) && toupper(meta->alph[i… in fm_alphabetCreate()
164 fm_getComplement (char c, uint8_t alph_type) in fm_getComplement() argument
166 if ( alph_type == fm_DNA ) { in fm_getComplement()
172 } else if ( alph_type == fm_AMINO) { in fm_getComplement()
|
| H A D | fm_sse.c | 76 if (cfg->meta->alph_type == fm_DNA) { in fm_configInit()
88 if (cfg->meta->alph_type == fm_DNA) { in fm_configInit()
103 if (cfg->meta->alph_type == fm_DNA) in fm_configInit()
124 if (cfg->meta->alph_type == fm_DNA) { in fm_configInit()
235 if (meta->alph_type == fm_DNA ) { in fm_getOccCount()
428 if (meta->alph_type == fm_DNA ) { in fm_getOccCountLT()
|
| H A D | makehmmerdb.c | 270 if (meta->alph_type == fm_DNA) { in buildAndWriteFMIndex()
288 if (meta->alph_type == fm_DNA ) { in buildAndWriteFMIndex()
443 meta->alph_type = fm_DNA; in main()
491 meta->alph_type = fm_AMINO; in main()
497 meta->alph_type = fm_DNA; in main()
504 meta->alph_type = fm_DNA; in main()
507 meta->alph_type = fm_AMINO; in main()
662 if ( meta->alph_type == fm_DNA) { in main()
731 fwrite(&(meta->alph_type), sizeof(meta->alph_type), 1, fp) != 1 || in main()
|
| H A D | hmmerfm-exactmatch.c | 98 if (meta->alph_type == fm_DNA) alph = "dna"; in output_header()
99 else if (meta->alph_type == fm_AMINO) alph = "amino"; in output_header()
158 uint8_t c = fm_getChar( cfg->meta->alph_type, j, fm->BWT); in getFMHits()
281 if (meta->alph_type == fm_DNA) abc = esl_alphabet_Create(eslDNA); in main()
282 else if (meta->alph_type == fm_AMINO) abc = esl_alphabet_Create(eslAMINO); in main()
|
| H A D | fm_general.c | 248 fm_getChar(uint8_t alph_type, int j, const uint8_t *B ) in fm_getChar() argument
252 if (alph_type == fm_DNA /* || alph_type == fm_RNA */) { in fm_getChar()
330 if (meta->alph_type == fm_DNA ) { in fm_convertRange2DSQ()
603 fread(&(meta->alph_type), sizeof(meta->alph_type), 1, meta->fp) != 1 || in fm_readFMmeta()
|
| H A D | hmmer.h | 904 uint8_t alph_type; member
1777 extern int fm_getComplement (char c, uint8_t alph_type);
1787 extern uint8_t fm_getChar(uint8_t alph_type, int j, const uint8_t *B );
|
| H A D | fm_ssv.c | 135 c = fm_getChar( fm_cfg->meta->alph_type, j, fmf->BWT); in FM_backtrackSeed()
|
| H A D | nhmmer.c | 727 …if ( ! ( fm_meta->alph_type == fm_DNA && (fm_meta->alph_size > 0 && fm_meta->alph_size < 30) ) ) { in serial_master()
|
| /dports/biology/hmmer/hmmer-3.3/src/ |
| H A D | fm_alphabet.c | 35 if ( meta->alph_type == fm_DNA) { in fm_alphabetCreate()
43 } else if ( meta->alph_type == fm_AMINO) { in fm_alphabetCreate()
53 if ( meta->alph_type == fm_DNA /*|| meta->alph_type == fm_DNA_full*/) in fm_alphabetCreate()
59 if ( meta->alph_type == fm_DNA) { in fm_alphabetCreate()
86 } else if ( meta->alph_type == fm_AMINO) { in fm_alphabetCreate()
97 …if ( (meta->alph_type == fm_DNA /*|| meta->alph_type == fm_DNA_full*/) && toupper(meta->alph[i… in fm_alphabetCreate()
164 fm_getComplement (char c, uint8_t alph_type) in fm_getComplement() argument
166 if ( alph_type == fm_DNA ) { in fm_getComplement()
172 } else if ( alph_type == fm_AMINO) { in fm_getComplement()
|
| H A D | fm_sse.c | 76 if (cfg->meta->alph_type == fm_DNA) { in fm_configInit()
88 if (cfg->meta->alph_type == fm_DNA) { in fm_configInit()
103 if (cfg->meta->alph_type == fm_DNA) in fm_configInit()
124 if (cfg->meta->alph_type == fm_DNA) { in fm_configInit()
235 if (meta->alph_type == fm_DNA ) { in fm_getOccCount()
428 if (meta->alph_type == fm_DNA ) { in fm_getOccCountLT()
|
| H A D | makehmmerdb.c | 270 if (meta->alph_type == fm_DNA) { in buildAndWriteFMIndex()
288 if (meta->alph_type == fm_DNA ) { in buildAndWriteFMIndex()
443 meta->alph_type = fm_DNA; in main()
491 meta->alph_type = fm_AMINO; in main()
497 meta->alph_type = fm_DNA; in main()
504 meta->alph_type = fm_DNA; in main()
507 meta->alph_type = fm_AMINO; in main()
662 if ( meta->alph_type == fm_DNA) { in main()
731 fwrite(&(meta->alph_type), sizeof(meta->alph_type), 1, fp) != 1 || in main()
|
| H A D | hmmerfm-exactmatch.c | 98 if (meta->alph_type == fm_DNA) alph = "dna"; in output_header()
99 else if (meta->alph_type == fm_AMINO) alph = "amino"; in output_header()
158 uint8_t c = fm_getChar( cfg->meta->alph_type, j, fm->BWT); in getFMHits()
281 if (meta->alph_type == fm_DNA) abc = esl_alphabet_Create(eslDNA); in main()
282 else if (meta->alph_type == fm_AMINO) abc = esl_alphabet_Create(eslAMINO); in main()
|
| H A D | fm_general.c | 248 fm_getChar(uint8_t alph_type, int j, const uint8_t *B ) in fm_getChar() argument
252 if (alph_type == fm_DNA /* || alph_type == fm_RNA */) { in fm_getChar()
330 if (meta->alph_type == fm_DNA ) { in fm_convertRange2DSQ()
603 fread(&(meta->alph_type), sizeof(meta->alph_type), 1, meta->fp) != 1 || in fm_readFMmeta()
|
| H A D | hmmer.h | 904 uint8_t alph_type; member
1777 extern int fm_getComplement (char c, uint8_t alph_type);
1787 extern uint8_t fm_getChar(uint8_t alph_type, int j, const uint8_t *B );
|
| H A D | fm_ssv.c | 135 c = fm_getChar( fm_cfg->meta->alph_type, j, fmf->BWT); in FM_backtrackSeed()
|
| H A D | nhmmer.c | 727 …if ( ! ( fm_meta->alph_type == fm_DNA && (fm_meta->alph_size > 0 && fm_meta->alph_size < 30) ) ) { in serial_master()
|