| /dports/biology/infernal/infernal-1.1.3/src/ |
| H A D | cmsearch.c | 1144 if(esl_opt_IsUsed(go, "-Z")) { in mpi_master()
1784 if(esl_opt_IsUsed(go, "--beta") && esl_opt_IsUsed(go, "--fbeta")) { in process_commandline()
1790 else if(esl_opt_IsUsed(go, "--beta")) { in process_commandline()
1811 if(esl_opt_IsUsed(go, "--max")) { in process_commandline()
1859 if(esl_opt_IsUsed(go, "--nohmm")) { in process_commandline()
1899 if(esl_opt_IsUsed(go, "--mid")) { in process_commandline()
1914 if(esl_opt_IsUsed(go, "--default")) { in process_commandline()
1920 if(esl_opt_IsUsed(go, "--rfam")) { in process_commandline()
1926 if(esl_opt_IsUsed(go, "--FZ")) { in process_commandline()
1932 if(esl_opt_IsUsed(go, "--hmmonly")) { in process_commandline()
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| H A D | cmscan.c | 481 if(esl_opt_IsUsed(go, "-Z")) { in serial_master()
1322 if(esl_opt_IsUsed(go, "-Z")) { in mpi_master()
1706 if(esl_opt_IsUsed(go, "-Z")) { in mpi_worker()
2100 if(esl_opt_IsUsed(go, "--beta") && esl_opt_IsUsed(go, "--fbeta")) { in process_commandline()
2130 if(esl_opt_IsUsed(go, "--oclan")) { in process_commandline()
2144 if(esl_opt_IsUsed(go, "--max")) { in process_commandline()
2192 if(esl_opt_IsUsed(go, "--nohmm")) { in process_commandline()
2232 if(esl_opt_IsUsed(go, "--mid")) { in process_commandline()
2253 if(esl_opt_IsUsed(go, "--rfam")) { in process_commandline()
2259 if(esl_opt_IsUsed(go, "--FZ")) { in process_commandline()
[all …]
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| H A D | cmbuild.c | 700 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
796 if (esl_opt_IsUsed(go, "-o")) { in init_cfg()
868 if(esl_opt_IsUsed(go, "--p7prior")) { in init_cfg()
989 (! esl_opt_IsUsed (go, "--prior"))) { in process_build_workunit()
1570 if(esl_opt_IsUsed(go, "--n2omega")) { /* user set --n2omega, use that */ in build_model()
1883 if(esl_opt_IsUsed(go, "--refine")) { in configure_model()
2016 if(esl_opt_IsUsed(go, "--ElL")) { in build_and_calibrate_p7_filter()
2019 else if(esl_opt_IsUsed(go, "--Elcmult")) { in build_and_calibrate_p7_filter()
2023 if(esl_opt_IsUsed(go, "--EgL")) { in build_and_calibrate_p7_filter()
2026 else if(esl_opt_IsUsed(go, "--Egcmult")) { in build_and_calibrate_p7_filter()
[all …]
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| H A D | cmstat.c | 126 if (esl_opt_IsUsed(go, "-E")) { output_mode = OUTMODE_BITSCORES_E; } in main()
127 else if(esl_opt_IsUsed(go, "-P")) { output_mode = OUTMODE_BITSCORES_P; } in main()
128 else if(esl_opt_IsUsed(go, "-T")) { output_mode = OUTMODE_EVALUES; } in main()
129 else if(esl_opt_IsUsed(go, "--cut_ga")) { output_mode = OUTMODE_GA; } in main()
130 else if(esl_opt_IsUsed(go, "--cut_tc")) { output_mode = OUTMODE_TC; } in main()
131 else if(esl_opt_IsUsed(go, "--cut_nc")) { output_mode = OUTMODE_NC; } in main()
183 if(! esl_opt_IsUsed(go, "--key")) { in main()
262 …if(esl_opt_IsUsed(go, "-E")) cm_Fail("-E requires E-value statistics (from cmcalibrate), mod… in output_stats()
263 …if(esl_opt_IsUsed(go, "-T")) cm_Fail("-T requires E-value statistics (from cmcalibrate), mod… in output_stats()
264 …if(esl_opt_IsUsed(go, "--cut_ga")) cm_Fail("--cut_ga requires E-value statistics (from cmcalibrate… in output_stats()
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| /dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
| H A D | alimask.c | 116 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in process_commandline()
147 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in output_header()
172 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
279 keep_mm = esl_opt_IsUsed(go, "--apendmask"); in main()
303 if (esl_opt_IsUsed(go, "--alirange")) { in main()
342 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in main()
347 if (esl_opt_IsUsed(go, "-o")) in main()
364 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in main()
377 …if (esl_opt_IsUsed(go, "--modelrange") || esl_opt_IsUsed(go, "--model2ali") || esl_opt_IsUsed(go, … in main()
395 if ( esl_opt_IsUsed(go, "--model2ali") ) { in main()
[all …]
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| H A D | hmmc2.c | 121 …if (esl_opt_IsUsed(sopt, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n"…
122 …if (esl_opt_IsUsed(sopt, "--noali") && fprintf(ofp, "# show alignments in output: no\n")…
123 …if (esl_opt_IsUsed(sopt, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimi…
125 …if (esl_opt_IsUsed(sopt, "--popen") && fprintf(ofp, "# gap open probability: %f\n",…
126 …if (esl_opt_IsUsed(sopt, "--pextend") && fprintf(ofp, "# gap extend probability: %f\n",…
127 …if (esl_opt_IsUsed(sopt, "--mx") && fprintf(ofp, "# subst score matrix (built-in): %s\n",…
128 …if (esl_opt_IsUsed(sopt, "--mxfile") && fprintf(ofp, "# subst score matrix (file): %s\n",…
129 …if (esl_opt_IsUsed(sopt, "-E") && fprintf(ofp, "# sequence reporting threshold: E-valu…
130 …if (esl_opt_IsUsed(sopt, "-T") && fprintf(ofp, "# sequence reporting threshold: score …
155 if (esl_opt_IsUsed(sopt, "--seed")) {
[all …]
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| H A D | hmmbuild.c | 348 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
529 if (esl_opt_IsUsed(go, "-o")) in usual_master()
582 pextend = esl_opt_IsUsed(go, "--pextend") ? esl_opt_GetReal(go, "--pextend") : 0.4; in usual_master()
588 if ( esl_opt_IsUsed(go, "--singlemx") ) { in usual_master()
593 if ( !esl_opt_IsUsed(go, "--mx") ) mx = "DNA1"; in usual_master()
599 if (esl_opt_IsUsed(go, "--popen") ) info[i].bld->popen = popen; in usual_master()
600 if (esl_opt_IsUsed(go, "--pextend")) info[i].bld->pextend = pextend; in usual_master()
726 if (esl_opt_IsUsed(go, "-o")) in mpi_master()
959 if ( msa->nseq == 1 && esl_opt_IsUsed(go, "--singlemx")) { in mpi_worker()
1038 if ( msa->nseq == 1 && esl_opt_IsUsed(go, "--singlemx")) { in serial_loop()
[all …]
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| H A D | nhmmer.c | 379 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
436 if (esl_opt_IsUsed(go, "--restrictdb_stkey") ) in main()
439 if (esl_opt_IsUsed(go, "--restrictdb_n") ) in main()
527 …if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")… in serial_master()
685 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in serial_master()
689 if (esl_opt_IsUsed(go, "--ssifile")) in serial_master()
923 if (! esl_opt_IsUsed(go, "--restrictdb_stkey") ) in serial_master()
997 if ( esl_opt_IsUsed(go, "--watson") ) in serial_master()
999 else if ( esl_opt_IsUsed(go, "--crick") ) in serial_master()
1006 if ( esl_opt_IsUsed(go, "--block_length") ) in serial_master()
[all …]
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| H A D | nhmmscan.c | 218 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
219 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
223 …if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n") … in output_header()
224 …if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") … in output_header()
225 …if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimite… in output_header()
249 …if (esl_opt_IsUsed(go, "--crick") && fprintf(ofp, "# search only bottom strand: on\n") … in output_header()
252 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
337 …if (esl_opt_IsUsed(go, "--w_beta")) { if ( ( window_beta = esl_opt_GetReal(go, "--w_beta") ) <… in serial_master()
338 …if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")… in serial_master()
470 if ( esl_opt_IsUsed(go, "--watson") ) in serial_master()
[all …]
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| H A D | jackhmmer.c | 290 …if (esl_opt_IsUsed(go, "-N") && fprintf(ofp, "# maximum iterations set to: %d\n", … in output_header()
291 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
292 …if (esl_opt_IsUsed(go, "-A") && fprintf(ofp, "# MSA of hits saved to file: %s\n", … in output_header()
293 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
294 …if (esl_opt_IsUsed(go, "--domtblout") && fprintf(ofp, "# per-dom hits tabular output: %s\n", … in output_header()
295 …if (esl_opt_IsUsed(go, "--chkhmm") && fprintf(ofp, "# HMM checkpoint files output: %s-<i>.… in output_header()
296 …if (esl_opt_IsUsed(go, "--chkali") && fprintf(ofp, "# MSA checkpoint files output: %s-<i>.… in output_header()
297 …if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n")… in output_header()
298 …if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") … in output_header()
299 …if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimit… in output_header()
[all …]
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| H A D | phmmer.c | 241 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
242 …if (esl_opt_IsUsed(go, "-A") && fprintf(ofp, "# MSA of hits saved to file: %s\n", … in output_header()
243 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
244 …if (esl_opt_IsUsed(go, "--domtblout") && fprintf(ofp, "# per-dom hits tabular output: %s\n", … in output_header()
284 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
329 if (esl_opt_IsUsed(go, "--restrictdb_stkey") ) in main()
332 if (esl_opt_IsUsed(go, "--restrictdb_n") ) in main()
465 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in serial_master()
466 if (esl_opt_IsUsed(go, "--ssifile")) in serial_master()
962 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in mpi_master()
[all …]
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| H A D | hmmsearch.c | 226 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
227 …if (esl_opt_IsUsed(go, "-A") && fprintf(ofp, "# MSA of all hits saved to file: %s\n", … in output_header()
228 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
258 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
296 if (esl_opt_IsUsed(go, "--restrictdb_stkey") ) in main()
299 if (esl_opt_IsUsed(go, "--restrictdb_n") ) in main()
399 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in serial_master()
400 if (esl_opt_IsUsed(go, "--ssifile")) in serial_master()
477 if (! esl_opt_IsUsed(go, "--restrictdb_stkey") ) in serial_master()
855 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in mpi_master()
[all …]
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| H A D | hmmscan.c | 215 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
216 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
217 …if (esl_opt_IsUsed(go, "--domtblout") && fprintf(ofp, "# per-dom hits tabular output: %s\n", … in output_header()
219 …if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n") … in output_header()
220 …if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") … in output_header()
221 …if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimite… in output_header()
223 …if (esl_opt_IsUsed(go, "-E") && fprintf(ofp, "# profile reporting threshold: E-value … in output_header()
224 …if (esl_opt_IsUsed(go, "-T") && fprintf(ofp, "# profile reporting threshold: score >=… in output_header()
225 …if (esl_opt_IsUsed(go, "--domE") && fprintf(ofp, "# domain reporting threshold: E-value … in output_header()
226 …if (esl_opt_IsUsed(go, "--domT") && fprintf(ofp, "# domain reporting threshold: score >=… in output_header()
[all …]
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| H A D | hmmpgmd.c | 136 …if (esl_opt_IsUsed(go, "--master") && !(esl_opt_IsUsed(go, "--seqdb") || esl_opt_IsUsed(go, "--hmm… in process_commandline()
168 if (esl_opt_IsUsed(go, "--master")) master_process(go); in main()
169 else if (esl_opt_IsUsed(go, "--worker")) worker_process(go); in main()
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| H A D | hmmpgmd_shard.c | 137 …if (esl_opt_IsUsed(go, "--master") && !(esl_opt_IsUsed(go, "--seqdb") || esl_opt_IsUsed(go, "--hmm… in process_commandline()
169 if (esl_opt_IsUsed(go, "--master")) master_process_shard(go); in main()
170 else if (esl_opt_IsUsed(go, "--worker")) worker_process_shard(go); in main()
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| /dports/biology/hmmer/hmmer-3.3/src/ |
| H A D | alimask.c | 116 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in process_commandline()
147 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in output_header()
172 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
279 keep_mm = esl_opt_IsUsed(go, "--apendmask"); in main()
303 if (esl_opt_IsUsed(go, "--alirange")) { in main()
342 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in main()
347 if (esl_opt_IsUsed(go, "-o")) in main()
364 if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) { in main()
377 …if (esl_opt_IsUsed(go, "--modelrange") || esl_opt_IsUsed(go, "--model2ali") || esl_opt_IsUsed(go, … in main()
395 if ( esl_opt_IsUsed(go, "--model2ali") ) { in main()
[all …]
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| H A D | hmmc2.c | 121 …if (esl_opt_IsUsed(sopt, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n"…
122 …if (esl_opt_IsUsed(sopt, "--noali") && fprintf(ofp, "# show alignments in output: no\n")…
123 …if (esl_opt_IsUsed(sopt, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimi…
125 …if (esl_opt_IsUsed(sopt, "--popen") && fprintf(ofp, "# gap open probability: %f\n",…
126 …if (esl_opt_IsUsed(sopt, "--pextend") && fprintf(ofp, "# gap extend probability: %f\n",…
127 …if (esl_opt_IsUsed(sopt, "--mx") && fprintf(ofp, "# subst score matrix (built-in): %s\n",…
128 …if (esl_opt_IsUsed(sopt, "--mxfile") && fprintf(ofp, "# subst score matrix (file): %s\n",…
129 …if (esl_opt_IsUsed(sopt, "-E") && fprintf(ofp, "# sequence reporting threshold: E-valu…
130 …if (esl_opt_IsUsed(sopt, "-T") && fprintf(ofp, "# sequence reporting threshold: score …
155 if (esl_opt_IsUsed(sopt, "--seed")) {
[all …]
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| H A D | hmmbuild.c | 348 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
529 if (esl_opt_IsUsed(go, "-o")) in usual_master()
582 pextend = esl_opt_IsUsed(go, "--pextend") ? esl_opt_GetReal(go, "--pextend") : 0.4; in usual_master()
588 if ( esl_opt_IsUsed(go, "--singlemx") ) { in usual_master()
593 if ( !esl_opt_IsUsed(go, "--mx") ) mx = "DNA1"; in usual_master()
599 if (esl_opt_IsUsed(go, "--popen") ) info[i].bld->popen = popen; in usual_master()
600 if (esl_opt_IsUsed(go, "--pextend")) info[i].bld->pextend = pextend; in usual_master()
726 if (esl_opt_IsUsed(go, "-o")) in mpi_master()
959 if ( msa->nseq == 1 && esl_opt_IsUsed(go, "--singlemx")) { in mpi_worker()
1038 if ( msa->nseq == 1 && esl_opt_IsUsed(go, "--singlemx")) { in serial_loop()
[all …]
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| H A D | nhmmer.c | 379 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
436 if (esl_opt_IsUsed(go, "--restrictdb_stkey") ) in main()
439 if (esl_opt_IsUsed(go, "--restrictdb_n") ) in main()
527 …if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")… in serial_master()
685 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in serial_master()
689 if (esl_opt_IsUsed(go, "--ssifile")) in serial_master()
923 if (! esl_opt_IsUsed(go, "--restrictdb_stkey") ) in serial_master()
997 if ( esl_opt_IsUsed(go, "--watson") ) in serial_master()
999 else if ( esl_opt_IsUsed(go, "--crick") ) in serial_master()
1006 if ( esl_opt_IsUsed(go, "--block_length") ) in serial_master()
[all …]
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| H A D | nhmmscan.c | 218 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
219 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
223 …if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n") … in output_header()
224 …if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") … in output_header()
225 …if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimite… in output_header()
249 …if (esl_opt_IsUsed(go, "--crick") && fprintf(ofp, "# search only bottom strand: on\n") … in output_header()
252 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
337 …if (esl_opt_IsUsed(go, "--w_beta")) { if ( ( window_beta = esl_opt_GetReal(go, "--w_beta") ) <… in serial_master()
338 …if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")… in serial_master()
470 if ( esl_opt_IsUsed(go, "--watson") ) in serial_master()
[all …]
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| H A D | jackhmmer.c | 290 …if (esl_opt_IsUsed(go, "-N") && fprintf(ofp, "# maximum iterations set to: %d\n", … in output_header()
291 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
292 …if (esl_opt_IsUsed(go, "-A") && fprintf(ofp, "# MSA of hits saved to file: %s\n", … in output_header()
293 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
294 …if (esl_opt_IsUsed(go, "--domtblout") && fprintf(ofp, "# per-dom hits tabular output: %s\n", … in output_header()
295 …if (esl_opt_IsUsed(go, "--chkhmm") && fprintf(ofp, "# HMM checkpoint files output: %s-<i>.… in output_header()
296 …if (esl_opt_IsUsed(go, "--chkali") && fprintf(ofp, "# MSA checkpoint files output: %s-<i>.… in output_header()
297 …if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n")… in output_header()
298 …if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") … in output_header()
299 …if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimit… in output_header()
[all …]
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| H A D | phmmer.c | 241 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
242 …if (esl_opt_IsUsed(go, "-A") && fprintf(ofp, "# MSA of hits saved to file: %s\n", … in output_header()
243 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
244 …if (esl_opt_IsUsed(go, "--domtblout") && fprintf(ofp, "# per-dom hits tabular output: %s\n", … in output_header()
284 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
329 if (esl_opt_IsUsed(go, "--restrictdb_stkey") ) in main()
332 if (esl_opt_IsUsed(go, "--restrictdb_n") ) in main()
465 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in serial_master()
466 if (esl_opt_IsUsed(go, "--ssifile")) in serial_master()
962 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in mpi_master()
[all …]
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| H A D | hmmsearch.c | 226 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
227 …if (esl_opt_IsUsed(go, "-A") && fprintf(ofp, "# MSA of all hits saved to file: %s\n", … in output_header()
228 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
258 if (esl_opt_IsUsed(go, "--seed")) { in output_header()
296 if (esl_opt_IsUsed(go, "--restrictdb_stkey") ) in main()
299 if (esl_opt_IsUsed(go, "--restrictdb_n") ) in main()
399 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in serial_master()
400 if (esl_opt_IsUsed(go, "--ssifile")) in serial_master()
477 if (! esl_opt_IsUsed(go, "--restrictdb_stkey") ) in serial_master()
855 if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) { in mpi_master()
[all …]
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| H A D | hmmscan.c | 215 …if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", … in output_header()
216 …if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", … in output_header()
217 …if (esl_opt_IsUsed(go, "--domtblout") && fprintf(ofp, "# per-dom hits tabular output: %s\n", … in output_header()
219 …if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n") … in output_header()
220 …if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") … in output_header()
221 …if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimite… in output_header()
223 …if (esl_opt_IsUsed(go, "-E") && fprintf(ofp, "# profile reporting threshold: E-value … in output_header()
224 …if (esl_opt_IsUsed(go, "-T") && fprintf(ofp, "# profile reporting threshold: score >=… in output_header()
225 …if (esl_opt_IsUsed(go, "--domE") && fprintf(ofp, "# domain reporting threshold: E-value … in output_header()
226 …if (esl_opt_IsUsed(go, "--domT") && fprintf(ofp, "# domain reporting threshold: score >=… in output_header()
[all …]
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| H A D | hmmpgmd.c | 136 …if (esl_opt_IsUsed(go, "--master") && !(esl_opt_IsUsed(go, "--seqdb") || esl_opt_IsUsed(go, "--hmm… in process_commandline()
168 if (esl_opt_IsUsed(go, "--master")) master_process(go); in main()
169 else if (esl_opt_IsUsed(go, "--worker")) worker_process(go); in main()
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