/dports/biology/mapm3/mapm3-3.0_1/mapm/ |
H A D | chroms.c | 73 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++) { [all …]
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H A D | auto_cmd.c | 82 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() [all …]
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H A D | print.c | 75 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; [all …]
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/dports/biology/recombine/recombine1.41/ |
H A D | filetran | 49 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++) { [all …]
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/dports/biology/migrate/migrate-3.6.11/src/ |
H A D | data.c | 163 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() [all …]
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H A D | migevents.c | 81 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() [all …]
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H A D | mutationmodel.c | 189 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() [all …]
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H A D | migrate_mpi.c | 211 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() [all …]
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H A D | fst.c | 89 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() [all …]
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H A D | skyline.c | 379 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() [all …]
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/dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
H A D | region.cpp | 96 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 [all …]
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H A D | region.h | 103 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 [all …]
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/dports/net/gnu-dico/dico-2.10/grecs/src/ |
H A D | diag.c | 31 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() [all …]
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H A D | format.c | 214 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() [all …]
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/dports/sysutils/direvent/direvent-5.2/grecs/src/ |
H A D | diag.c | 31 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() [all …]
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H A D | format.c | 214 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() [all …]
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/dports/sysutils/pies/pies-1.5/grecs/src/ |
H A D | diag.c | 31 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() [all …]
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H A D | format.c | 214 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() [all …]
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/dports/sysutils/eclat/eclat-2.0/grecs/src/ |
H A D | diag.c | 31 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 …]
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H A D | format.c | 214 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; [all …]
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/dports/net/gnu-dico/dico-2.10/dicod/ |
H A D | main.c | 922 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() [all …]
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H A D | acl.c | 43 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() [all …]
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/dports/sysutils/eclat/eclat-2.0/lib/ |
H A D | diag.c | 42 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); [all …]
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/dports/sysutils/eclat/eclat-2.0/src/ |
H A D | config.c | 69 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 [all …]
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/dports/biology/migrate/migrate-3.6.11/example/ |
H A D | sumfile | 6 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 ################ [all …]
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