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/dports/biology/mapm3/mapm3-3.0_1/mapm/
H A Dchroms.c73 int locus; in framework_marker()
83 if (locus==frame->locus[j]) return(TRUE);
225 int locus; in assigned()
229 int locus; in assignment_state()
233 int locus; in assignment_chrom()
247 int locus; in anchor_locus()
649 sf(ps,PLACE_INSANE,locus+1,locname(locus,TRUE));
653 sf(ps,PLACE_ISFRAME,locus+1,locname(locus,TRUE),
874 for (locus=0; locus<num_markers; locus++) {
913 for (locus=0; locus< raw.num_markers; locus++) {
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H A Dauto_cmd.c82 unarray(locus,int); in set_anchors()
211 unarray(locus,int); in list_mapping()
238 if (!is_assignable(locus[i],ANY_CHROM,TRUE)) locus[i]=NO_LOCUS; in assign()
243 unarray(locus, int); in assign()
295 unarray(locus,int); in unassign()
337 if (!is_placeable(locus[i],ANY_CHROM)) locus[i]=NO_LOCUS; in place()
344 if (assigned_to(locus[i],chrom) && is_placeable(locus[i],chrom)) in place()
345 { chrom_locus[n_to_place++]=locus[i]; locus[i]=NO_LOCUS; } in place()
421 unarray(locus,int); in place()
515 if (!is_placeable(locus[i],ANY_CHROM)) locus[i]=NO_LOCUS; in place_together()
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H A Dprint.c75 raw.data.f2.allele[map->locus[locus-1]][indiv],
76 raw.data.f2.allele[map->locus[locus]] [indiv],
77 raw.data.f2.allele[map->locus[locus+1]][indiv],
180 locs2str(map->locus[i],map->locus[i+1]),
285 int locus; in loc2str()
303 int locus; in locname()
464 int locus; in region2str()
475 int locus; in genetics2str()
794 int locus; in print_geno_line()
914 for (locus=haplo_first[map->locus[i]]; locus!=NO_LOCUS;
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/dports/biology/recombine/recombine1.41/
H A Dfiletran49 LOCUSLOOP: for($locus = 0; $locus < $numloci; $locus++) {
52 for(; $locus < $numloci; $locus++) {
68 for($locus = 0; $locus < $numloci; $locus++) {
73 $numseq[$locus] = $dataline;
74 $numseq[$locus] =~ s/\n$//;
75 print TARGET "$numseq[$locus] $numbases[$locus]\n";
120 for($locus = 0; $locus < $numloci; $locus++) {
125 ($numseq[$locus],$numbases[$locus]) = split(" ",$dataline);
127 $data[$locus][$seq] = "";
155 for($locus = 0; $locus < $numloci; $locus++) {
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/dports/biology/migrate/migrate-3.6.11/src/
H A Ddata.c163 for (locus = 0; locus < loci; locus++) in destroy_data()
177 for(locus=0; locus < loci; locus++) in destroy_data()
184 for(locus=0; locus < loci; locus++) in destroy_data()
218 for(locus=0;locus<data->loci;locus++) in destroy_data()
397 for (locus=0; locus < data->loci; locus++) in get_new_data()
431 for(locus=0;locus<data->loci;locus++) in get_data()
512 for (locus=0; locus < data->loci; locus++) in get_data()
563 for(locus=0;locus<loci;locus++) in init_data_structure1()
1531 for(locus=0;locus<data->loci;locus++) in read_hapmap_genotypes()
1634 for(locus=0;locus<data->loci;locus++) in read_hapmap()
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H A Dmigevents.c81 long locus; in destroy_mighist() local
85 for(locus=0; locus < world->loci; locus++) in destroy_mighist()
162 for (locus = 0; locus < world->loci; locus++) in print_mighist_output()
183 for (locus = 0; locus < world->loci; locus++) in print_mighist_output()
275 for (locus = 0; locus < loci1; locus++) in print_mighist_output()
405 for (locus = 0; locus < world->loci; locus++) in setup_mig_coal_events()
436 for (locus = 0; locus < world->loci; locus++) in destroy_mig_coal_events()
595 for(locus=0; locus < world->loci + sumloc; locus++) in print_event_values_tofile()
632 for(locus=0; locus < world->loci; locus++) in prepare_event_values()
694 for (locus = 0; locus < world->loci; locus++) in prepare_event_values()
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H A Dmutationmodel.c189 const unsigned long locus = world->locus; in finish_mutationmodel() local
216 long locus; in print_mutationrate_weights() local
229 for (locus=0; locus < loci; locus++) in print_mutationrate_weights()
231 fprintf(file,"%5li % 5.5f % 6li\n",locus+1, murates[locus], segregs[locus]); in print_mutationrate_weights()
232 mumean += (float) (murates[locus] - mumean)/(locus+1); in print_mutationrate_weights()
233 segregmean += (segregs[locus] - segregmean)/(locus+1); in print_mutationrate_weights()
242 for (locus=0; locus < loci; locus++) in print_mutationrate_weights()
244 …5li % 5.5f %2.8f % 6li\n",locus+1, murates[locus], wattersons[locus], segreg… in print_mutationrate_weights()
245 mumean += (float) (murates[locus] - mumean)/(locus+1); in print_mutationrate_weights()
246 wamean += (float) (wattersons[locus] - wamean)/(locus+1); in print_mutationrate_weights()
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H A Dmigrate_mpi.c211 for (locus = 0; locus < minnodes; locus++) in mpi_runloci_master()
838 for (locus = 0; locus < world->loci; locus++) in mpi_likelihood_master()
1555 for(locus=0; locus<data->loci; locus++) in pack_databuffer()
1587 for(locus=0;locus<data->loci; ++locus) in pack_databuffer()
1624 for(locus=0;locus<data->loci;locus++) in pack_databuffer()
1645 for(locus=0;locus<data->loci;locus++) in pack_databuffer()
1836 for(locus=0; locus<data->loci; locus++) in unpack_databuffer()
1936 for(locus=0;locus<data->loci;locus++) in unpack_databuffer()
1954 for(locus=0;locus<data->loci;locus++) in unpack_databuffer()
1972 for(locus=0;locus<data->loci;locus++) in unpack_databuffer()
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H A Dfst.c89 long pop, locus; in calc_fst() local
119 for (locus = 0; locus < world->loci; locus++) in calc_fst()
179 long pop, locus, ind, a; in frequencies() local
185 for (locus = 0; locus < loci; locus++) in frequencies()
191 if (data[pop][ind][locus][0][0] != '?') in frequencies()
224 fw[pop] += f[pop][locus][i] * f[pop][locus][i]; in calc_fw()
239 fb[zz] += f[p1][locus][i] * f[p2][locus][i]; in calc_fb()
256 data->seq[0]->sites[locus] * (data->numind[pop][locus] * in calc_seq_fw()
259 for (i = 0; i < data->numind[pop][locus]; i++) in calc_seq_fw()
291 (MYREAL) data->seq[0]->sites[locus] * data->numind[p1][locus] * in calc_seq_fb()
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H A Dskyline.c379 for (locus = 0; locus < world->loci; locus++) in setup_expected_events()
406 for (locus = 0; locus < world->loci; locus++) in destroy_expected_events()
457 long locus; in read_expected_values_fromfile() local
525 long locus; in print_expected_values_tofile() local
570 for(locus=0; locus < world->loci + sumloc; locus++) in print_expected_values_tofile()
594 long locus; in prepare_expected_values() local
609 for(locus=0; locus < world->loci; locus++) in prepare_expected_values()
698 for (locus = 0; locus < world->loci; locus++) in prepare_expected_values()
753 long locus; in print_expected_values() local
773 for(locus=0; locus < world->loci+sumloc; locus++) in print_expected_values()
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/dports/biology/lamarc/lamarc-2.1.8/src/datalike/
H A Dregion.cpp96 for(locus = m_loci.begin(); locus != m_loci.end(); ++locus) in InitializeRegionalMappositionsUsingGlobalMappositions()
295 for (size_t locus=0; locus<phasesites.size(); locus++) in SetPhaseMarkers() local
340 for (size_t locus=0; locus<m_loci.size(); locus++) in HasLocus() local
363 for (size_t locus=0; locus<m_loci.size(); locus++) in GetNumFixedLoci() local
374 for (size_t locus=0; locus<m_loci.size(); locus++) in GetLocusIndex() local
394 for (size_t locus=0; locus<m_loci.size(); locus++) in GetLocus() local
409 for (size_t locus=0; locus < m_loci.size(); locus++) in GetNumSites() local
427 for (size_t locus=1; locus < m_loci.size(); locus++) in GetSiteSpan() local
489 for(locus = 0; locus < nloci; ++locus) in ToXML()
894 for (size_t locus=0; locus<m_loci.size(); locus++) in AnySimulatedLoci() local
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H A Dregion.h103 void SetOffset(long locus, long n);
122 Locus& GetLocus(long locus) {assert(ValidLocus(locus)); in GetLocus() argument
123 return m_loci[locus]; }; in GetLocus()
124 const Locus& GetLocus(long locus) const {assert(ValidLocus(locus)); in GetLocus() argument
125 return m_loci[locus]; }; in GetLocus()
145 long GetNmarkers(long locus) const {return m_loci[locus].GetNmarkers();}; in GetNmarkers() argument
146 long GetMapposition(long locus) const {return m_loci[locus].GetRegionalMapposition();}; in GetMapposition() argument
147 …long GetGlobalMapposition(long locus) const {return m_loci[locus].GetGlobalMapposition();}; in GetGlobalMapposition() argument
148 long GetOffset(long locus) const {return m_loci[locus].GetOffset();}; in GetOffset() argument
154 DataModel_ptr GetLocusDataModel(long locus) const {return m_loci[locus].GetDataModel(); }; in GetLocusDataModel() argument
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/dports/net/gnu-dico/dico-2.10/grecs/src/
H A Ddiag.c31 if (locus) { in default_print_diag()
86 locus->beg.file, in grecs_asprint_locus()
88 else if (strcmp(locus->beg.file, locus->end.file)) in grecs_asprint_locus()
90 locus->beg.file, in grecs_asprint_locus()
91 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
93 locus->end.line, locus->end.col); in grecs_asprint_locus()
94 else if (locus->beg.line != locus->end.line) in grecs_asprint_locus()
97 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
98 locus->end.line, locus->end.col); in grecs_asprint_locus()
99 else if (locus->beg.col != locus->end.col) in grecs_asprint_locus()
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H A Dformat.c214 else if (strcmp(locus->beg.file, locus->end.file)) in grecs_format_locus()
217 locus->beg.line, locus->beg.col, in grecs_format_locus()
219 locus->end.line, locus->end.col); in grecs_format_locus()
220 else if (locus->beg.line != locus->end.line) in grecs_format_locus()
223 locus->beg.line, locus->beg.col, in grecs_format_locus()
224 locus->end.line, locus->end.col); in grecs_format_locus()
225 else if (locus->beg.col != locus->end.col) in grecs_format_locus()
228 locus->beg.line, locus->beg.col, in grecs_format_locus()
354 locus = &node->locus; in grecs_format_node()
358 locus = &node->v.value->locus; in grecs_format_node()
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/dports/sysutils/direvent/direvent-5.2/grecs/src/
H A Ddiag.c31 if (locus) { in default_print_diag()
86 locus->beg.file, in grecs_asprint_locus()
88 else if (strcmp(locus->beg.file, locus->end.file)) in grecs_asprint_locus()
90 locus->beg.file, in grecs_asprint_locus()
91 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
93 locus->end.line, locus->end.col); in grecs_asprint_locus()
94 else if (locus->beg.line != locus->end.line) in grecs_asprint_locus()
97 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
98 locus->end.line, locus->end.col); in grecs_asprint_locus()
99 else if (locus->beg.col != locus->end.col) in grecs_asprint_locus()
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H A Dformat.c214 else if (strcmp(locus->beg.file, locus->end.file)) in grecs_format_locus()
217 locus->beg.line, locus->beg.col, in grecs_format_locus()
219 locus->end.line, locus->end.col); in grecs_format_locus()
220 else if (locus->beg.line != locus->end.line) in grecs_format_locus()
223 locus->beg.line, locus->beg.col, in grecs_format_locus()
224 locus->end.line, locus->end.col); in grecs_format_locus()
225 else if (locus->beg.col != locus->end.col) in grecs_format_locus()
228 locus->beg.line, locus->beg.col, in grecs_format_locus()
354 locus = &node->locus; in grecs_format_node()
358 locus = &node->v.value->locus; in grecs_format_node()
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/dports/sysutils/pies/pies-1.5/grecs/src/
H A Ddiag.c31 if (locus) { in default_print_diag()
86 locus->beg.file, in grecs_asprint_locus()
88 else if (strcmp(locus->beg.file, locus->end.file)) in grecs_asprint_locus()
90 locus->beg.file, in grecs_asprint_locus()
91 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
93 locus->end.line, locus->end.col); in grecs_asprint_locus()
94 else if (locus->beg.line != locus->end.line) in grecs_asprint_locus()
97 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
98 locus->end.line, locus->end.col); in grecs_asprint_locus()
99 else if (locus->beg.col != locus->end.col) in grecs_asprint_locus()
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H A Dformat.c214 else if (strcmp(locus->beg.file, locus->end.file)) in grecs_format_locus()
217 locus->beg.line, locus->beg.col, in grecs_format_locus()
219 locus->end.line, locus->end.col); in grecs_format_locus()
220 else if (locus->beg.line != locus->end.line) in grecs_format_locus()
223 locus->beg.line, locus->beg.col, in grecs_format_locus()
224 locus->end.line, locus->end.col); in grecs_format_locus()
225 else if (locus->beg.col != locus->end.col) in grecs_format_locus()
228 locus->beg.line, locus->beg.col, in grecs_format_locus()
354 locus = &node->locus; in grecs_format_node()
358 locus = &node->v.value->locus; in grecs_format_node()
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/dports/sysutils/eclat/eclat-2.0/grecs/src/
H A Ddiag.c31 if (locus) { in default_print_diag()
86 locus->beg.file, in grecs_asprint_locus()
88 else if (strcmp(locus->beg.file, locus->end.file)) in grecs_asprint_locus()
90 locus->beg.file, in grecs_asprint_locus()
91 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
92 locus->end.file, in grecs_asprint_locus()
93 locus->end.line, locus->end.col); in grecs_asprint_locus()
94 else if (locus->beg.line != locus->end.line) in grecs_asprint_locus()
97 locus->beg.line, locus->beg.col, in grecs_asprint_locus()
98 locus->end.line, locus->end.col); in grecs_asprint_locus()
[all …]
H A Dformat.c214 else if (strcmp(locus->beg.file, locus->end.file))
217 locus->beg.line, locus->beg.col,
219 locus->end.line, locus->end.col);
220 else if (locus->beg.line != locus->end.line)
223 locus->beg.line, locus->beg.col,
224 locus->end.line, locus->end.col);
225 else if (locus->beg.col != locus->end.col)
228 locus->beg.line, locus->beg.col,
354 locus = &node->locus;
358 locus = &node->v.value->locus;
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/dports/net/gnu-dico/dico-2.10/dicod/
H A Dmain.c922 cfg->locus = *locus; in user_db_config()
923 cfg->locus.beg.file = xstrdup(cfg->locus.beg.file); in user_db_config()
924 cfg->locus.end.file = xstrdup(cfg->locus.end.file); in user_db_config()
938 cfg->locus = *locus; in user_db_config()
939 cfg->locus.beg.file = xstrdup(cfg->locus.beg.file); in user_db_config()
1644 locus->beg.line, locus->beg.col, in _print_diag()
1646 locus->end.line, locus->end.col); in _print_diag()
1647 else if (locus->beg.line != locus->end.line) in _print_diag()
1650 locus->beg.line, locus->beg.col, in _print_diag()
1651 locus->end.line, locus->end.col); in _print_diag()
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H A Dacl.c43 grecs_locus_t locus; member
54 grecs_locus_t locus; member
85 acl->locus = *locus; in dicod_acl_create()
86 acl->locus.beg.file = strdup(acl->locus.beg.file); in dicod_acl_create()
87 acl->locus.end.file = strdup(acl->locus.end.file); in dicod_acl_create()
282 entry->locus = *locus; in parse_acl_line()
283 entry->locus.beg.file = strdup(entry->locus.beg.file); in parse_acl_line()
284 entry->locus.end.file = strdup(entry->locus.end.file); in parse_acl_line()
397 ent->locus.beg.file, ent->locus.beg.line, in _acl_check_cb()
451 if (locus) in dicod_acl_install()
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/dports/sysutils/eclat/eclat-2.0/lib/
H A Ddiag.c42 if (locus) {
45 locus->beg.file,
47 else if (strcmp(locus->beg.file, locus->end.file))
49 locus->beg.file,
50 locus->beg.line, locus->beg.col,
51 locus->end.file,
52 locus->end.line, locus->end.col);
53 else if (locus->beg.line != locus->end.line)
56 locus->beg.line, locus->beg.col,
57 locus->end.line, locus->end.col);
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/dports/sysutils/eclat/eclat-2.0/src/
H A Dconfig.c69 grecs_locus_t *locus, in cb_region() argument
101 grecs_locus_t *locus, in cb_format() argument
121 &value->v.arg.v[1]->locus); in cb_format()
127 grecs_locus_t *locus, in cb_define_format() argument
154 grecs_locus_t *locus, in cb_confirm() argument
216 &argval->locus); in cb_confirm()
240 grecs_locus_t *locus, in cb_ssl() argument
249 grecs_error (value ? &value->locus : locus, 0, in cb_ssl()
259 grecs_locus_t *locus, in cb_authentication_provider() argument
321 grecs_locus_t *locus, in cb_access_file() argument
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/dports/biology/migrate/migrate-3.6.11/example/
H A Dsumfile6 0 0 ####### locus 0, replicate 0 ################
4014 0 1 ####### locus 0, replicate 1 ################
8022 1 0 ####### locus 1, replicate 0 ################
12030 1 1 ####### locus 1, replicate 1 ################
16038 2 0 ####### locus 2, replicate 0 ################
20046 2 1 ####### locus 2, replicate 1 ################
24054 3 0 ####### locus 3, replicate 0 ################
28062 3 1 ####### locus 3, replicate 1 ################
32070 4 0 ####### locus 4, replicate 0 ################
36078 4 1 ####### locus 4, replicate 1 ################
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