| /dports/biology/infernal/infernal-1.1.3/src/ |
| H A D | cm_p7_domaindef.c | 154 if (ddef->mocc[j] - (ddef->btot[j] - ddef->btot[j-1]) < ddef->rt2) i = j; in p7_domaindef_GlocalByPosteriorHeuristics()
158 else if (ddef->mocc[j] - (ddef->etot[j] - ddef->etot[j-1]) < ddef->rt2) in p7_domaindef_GlocalByPosteriorHeuristics()
280 expected_n = ESL_MIN( (ddef->etot[z] - ddef->etot[i-1]), (ddef->btot[j] - ddef->btot[z-1])); in is_multidomain_region()
374 …p7_spensemble_Add(ddef->sp, t, ddef->tr->sqfrom[d]+ireg-1, ddef->tr->sqto[d]+ireg-1, ddef->tr->hmm… in glocal_region_trace_ensemble()
396 ddef->n2sc[pos] = logf(ddef->n2sc[pos] / (float) ddef->nsamples); in glocal_region_trace_ensemble()
400 …p7_spensemble_Cluster(ddef->sp, ddef->min_overlap, ddef->of_smaller, ddef->max_diagdiff, ddef->min… in glocal_region_trace_ensemble()
411 …nov = ESL_MIN(ddef->sp->sigc[d].j, ddef->sp->sigc[d2].j) - ESL_MAX(ddef->sp->sigc[d].i, ddef->sp->… in glocal_region_trace_ensemble()
413 …n = ESL_MIN(ddef->sp->sigc[d].j - ddef->sp->sigc[d].i + 1, ddef->sp->sigc[d2].j - ddef->sp->sig… in glocal_region_trace_ensemble()
542 if (ddef->tr->i[z] > 0) ddef->tr->i[z] += i-1; in glocal_rescore_isolated_domain()
546 if (ddef->ndom == ddef->nalloc) { in glocal_rescore_isolated_domain()
[all …]
|
| /dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
| H A D | p7_domaindef.c | 79 ddef->mocc = ddef->btot = ddef->etot = NULL; in p7_domaindef_Create()
90 ddef->mocc[0] = ddef->etot[0] = ddef->btot[0] = 0.; in p7_domaindef_Create()
288 if (ddef->mocc != NULL) free(ddef->mocc); in p7_domaindef_Destroy()
414 if (ddef->mocc[j] - (ddef->btot[j] - ddef->btot[j-1]) < ddef->rt2) i = j; in p7_domaindef_ByPosteriorHeuristics()
418 else if (ddef->mocc[j] - (ddef->etot[j] - ddef->etot[j-1]) < ddef->rt2) in p7_domaindef_ByPosteriorHeuristics()
540 expected_n = ESL_MIN( (ddef->etot[z] - ddef->etot[i-1]), (ddef->btot[j] - ddef->btot[z-1])); in is_multidomain_region()
624 …p7_spensemble_Add(ddef->sp, t, ddef->tr->sqfrom[d]+ireg-1, ddef->tr->sqto[d]+ireg-1, ddef->tr->hmm… in region_trace_ensemble()
642 ddef->n2sc[pos] = logf(ddef->n2sc[pos] / (float) ddef->nsamples); in region_trace_ensemble()
645 …p7_spensemble_Cluster(ddef->sp, ddef->min_overlap, ddef->of_smaller, ddef->max_diagdiff, ddef->min… in region_trace_ensemble()
858 if (ddef->ndom == ddef->nalloc) { in rescore_isolated_domain()
[all …]
|
| /dports/biology/hmmer/hmmer-3.3/src/ |
| H A D | p7_domaindef.c | 79 ddef->mocc = ddef->btot = ddef->etot = NULL; in p7_domaindef_Create()
90 ddef->mocc[0] = ddef->etot[0] = ddef->btot[0] = 0.; in p7_domaindef_Create()
288 if (ddef->mocc != NULL) free(ddef->mocc); in p7_domaindef_Destroy()
414 if (ddef->mocc[j] - (ddef->btot[j] - ddef->btot[j-1]) < ddef->rt2) i = j; in p7_domaindef_ByPosteriorHeuristics()
418 else if (ddef->mocc[j] - (ddef->etot[j] - ddef->etot[j-1]) < ddef->rt2) in p7_domaindef_ByPosteriorHeuristics()
540 expected_n = ESL_MIN( (ddef->etot[z] - ddef->etot[i-1]), (ddef->btot[j] - ddef->btot[z-1])); in is_multidomain_region()
624 …p7_spensemble_Add(ddef->sp, t, ddef->tr->sqfrom[d]+ireg-1, ddef->tr->sqto[d]+ireg-1, ddef->tr->hmm… in region_trace_ensemble()
642 ddef->n2sc[pos] = logf(ddef->n2sc[pos] / (float) ddef->nsamples); in region_trace_ensemble()
645 …p7_spensemble_Cluster(ddef->sp, ddef->min_overlap, ddef->of_smaller, ddef->max_diagdiff, ddef->min… in region_trace_ensemble()
858 if (ddef->ndom == ddef->nalloc) { in rescore_isolated_domain()
[all …]
|
| /dports/devel/cargo-c/cargo-c-0.9.6+cargo-0.58/cargo-crates/libgit2-sys-0.12.26+1.3.0/libgit2/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/sentry-cli/sentry-cli-1.71.0/cargo-crates/libgit2-sys-0.12.23+1.2.0/libgit2/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/git-absorb/git-absorb-0.6.6/cargo-crates/libgit2-sys-0.12.13+1.0.1/libgit2/src/ |
| H A D | diff_driver.c | 188 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
195 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
199 if (!ddef) in git_diff_driver_builtin()
202 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
207 if (ddef->fns && in git_diff_driver_builtin()
209 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
212 if (ddef->words && in git_diff_driver_builtin()
213 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/git-delta/delta-0.9.2/cargo-crates/libgit2-sys-0.12.24+1.3.0/libgit2/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/sysutils/vector/vector-0.10.0/cargo-crates/libgit2-sys-0.12.7+1.0.0/libgit2/src/ |
| H A D | diff_driver.c | 188 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
195 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
199 if (!ddef) in git_diff_driver_builtin()
202 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
207 if (ddef->fns && in git_diff_driver_builtin()
209 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
212 if (ddef->words && in git_diff_driver_builtin()
213 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/security/cargo-audit/rustsec-cargo-audit-v0.15.2/cargo-audit/cargo-crates/libgit2-sys-0.12.19+1.1.0/libgit2/src/ |
| H A D | diff_driver.c | 188 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
195 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
199 if (!ddef) in git_diff_driver_builtin()
202 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
207 if (ddef->fns && in git_diff_driver_builtin()
209 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
212 if (ddef->words && in git_diff_driver_builtin()
213 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/tokei/tokei-12.1.2/cargo-crates/libgit2-sys-0.12.17+1.1.0/libgit2/src/ |
| H A D | diff_driver.c | 188 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
195 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
199 if (!ddef) in git_diff_driver_builtin()
202 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
207 if (ddef->fns && in git_diff_driver_builtin()
209 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
212 if (ddef->words && in git_diff_driver_builtin()
213 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/gitui/gitui-0.10.1/cargo-crates/libgit2-sys-0.12.12+1.0.1/libgit2/src/ |
| H A D | diff_driver.c | 188 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
195 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
199 if (!ddef) in git_diff_driver_builtin()
202 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
207 if (ddef->fns && in git_diff_driver_builtin()
209 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
212 if (ddef->words && in git_diff_driver_builtin()
213 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/security/cargo-audit/rustsec-cargo-audit-v0.15.2/cargo-audit/cargo-crates/libgit2-sys-0.12.23+1.2.0/libgit2/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/cargo-generate/cargo-generate-0.9.0/cargo-crates/libgit2-sys-0.12.22+1.1.0/libgit2/src/ |
| H A D | diff_driver.c | 187 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
194 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
198 if (!ddef) in git_diff_driver_builtin()
201 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
206 if (ddef->fns && in git_diff_driver_builtin()
208 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
211 if (ddef->words && in git_diff_driver_builtin()
212 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/misc/broot/broot-1.7.0/cargo-crates/libgit2-sys-0.12.21+1.1.0/libgit2/src/ |
| H A D | diff_driver.c | 187 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
194 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
198 if (!ddef) in git_diff_driver_builtin()
201 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
206 if (ddef->fns && in git_diff_driver_builtin()
208 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
211 if (ddef->words && in git_diff_driver_builtin()
212 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/sysutils/onefetch/onefetch-2.10.2/cargo-crates/libgit2-sys-0.12.21+1.1.0/libgit2/src/ |
| H A D | diff_driver.c | 187 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
194 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
198 if (!ddef) in git_diff_driver_builtin()
201 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
206 if (ddef->fns && in git_diff_driver_builtin()
208 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
211 if (ddef->words && in git_diff_driver_builtin()
212 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/pijul/pijul-1.0.0.a55/cargo-crates/libgit2-sys-0.12.24+1.3.0/libgit2/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/textproc/mdbook-linkcheck/mdbook-linkcheck-0.7.6/cargo-crates/libgit2-sys-0.12.24+1.3.0/libgit2/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/lang/rust/rustc-1.58.1-src/vendor/libgit2-sys/libgit2/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/sysutils/exa/exa-0.10.1/cargo-crates/libgit2-sys-0.12.18+1.1.0/libgit2/src/ |
| H A D | diff_driver.c | 188 git_diff_driver_definition *ddef = NULL;
195 ddef = &builtin_defs[idx];
199 if (!ddef)
202 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0)
207 if (ddef->fns &&
209 drv, ddef->fns, ddef->flags)) < 0)
212 if (ddef->words &&
213 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0)
|
| /dports/devel/libgit2/libgit2-1.3.0/src/ |
| H A D | diff_driver.c | 192 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
199 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
203 if (!ddef) in git_diff_driver_builtin()
206 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
211 if (ddef->fns && in git_diff_driver_builtin()
213 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
216 if (ddef->words && in git_diff_driver_builtin()
217 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/textproc/bat/bat-0.18.3/cargo-crates/libgit2-sys-0.12.21+1.1.0/libgit2/src/ |
| H A D | diff_driver.c | 187 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
194 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
198 if (!ddef) in git_diff_driver_builtin()
201 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
206 if (ddef->fns && in git_diff_driver_builtin()
208 drv, ddef->fns, ddef->flags)) < 0) in git_diff_driver_builtin()
211 if (ddef->words && in git_diff_driver_builtin()
212 (error = git_regexp_compile(&drv->word_pattern, ddef->words, ddef->flags)) < 0) in git_diff_driver_builtin()
|
| /dports/devel/interactive_rebase_tool/git-interactive-rebase-tool-1.2.1/cargo-crates/libgit2-sys-0.7.11/libgit2/src/ |
| H A D | diff_driver.c | 187 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
193 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
197 if (!ddef) in git_diff_driver_builtin()
200 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
205 if (ddef->fns && in git_diff_driver_builtin()
207 drv, ddef->fns, ddef->flags | REG_EXTENDED)) < 0) in git_diff_driver_builtin()
210 if (ddef->words && in git_diff_driver_builtin()
212 &drv->word_pattern, ddef->words, ddef->flags | REG_EXTENDED))) in git_diff_driver_builtin()
|
| /dports/devel/R-cran-git2r/git2r/src/libgit2/src/ |
| H A D | diff_driver.c | 187 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
193 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
197 if (!ddef) in git_diff_driver_builtin()
200 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
205 if (ddef->fns && in git_diff_driver_builtin()
207 drv, ddef->fns, ddef->flags | REG_EXTENDED)) < 0) in git_diff_driver_builtin()
210 if (ddef->words && in git_diff_driver_builtin()
212 &drv->word_pattern, ddef->words, ddef->flags | REG_EXTENDED))) in git_diff_driver_builtin()
|
| /dports/devel/gbump/gbump-1.0.1/cargo-crates/libgit2-sys-0.9.1/libgit2/src/ |
| H A D | diff_driver.c | 187 git_diff_driver_definition *ddef = NULL; in git_diff_driver_builtin() local
194 ddef = &builtin_defs[idx]; in git_diff_driver_builtin()
198 if (!ddef) in git_diff_driver_builtin()
201 if ((error = diff_driver_alloc(&drv, NULL, ddef->name)) < 0) in git_diff_driver_builtin()
206 if (ddef->fns && in git_diff_driver_builtin()
208 drv, ddef->fns, ddef->flags | P_REG_EXTENDED)) < 0) in git_diff_driver_builtin()
211 if (ddef->words && in git_diff_driver_builtin()
213 &drv->word_pattern, ddef->words, ddef->flags | P_REG_EXTENDED))) in git_diff_driver_builtin()
|
| /dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/ |
| H A D | decoding.c | 160 p7_DomainDecoding(const P7_OPROFILE *om, const P7_OMX *oxf, const P7_OMX *oxb, P7_DOMAINDEF *ddef) in p7_DomainDecoding() argument
167 ddef->btot[0] = 0.0; in p7_DomainDecoding()
168 ddef->etot[0] = 0.0; in p7_DomainDecoding()
169 ddef->mocc[0] = 0.0; in p7_DomainDecoding()
173 ddef->btot[i] = ddef->btot[i-1] + in p7_DomainDecoding()
179 ddef->etot[i] = ddef->etot[i-1] + in p7_DomainDecoding()
185 ddef->mocc[i] = 1. - njcp; in p7_DomainDecoding()
187 ddef->L = oxf->L; in p7_DomainDecoding()
|