/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/kalign2/ |
H A D | kalign2_input.c | 189 aln = aln_alloc(aln); in detect_and_read_sequences() 240 aln->sl[numseq+i] = aln->sl[aln->sip[numseq+i][0]]; in detect_and_read_sequences() 1454 aln->s[i][aln->sl[i]] = 0; in read_sequences_clustal() 1571 aln->s[i][aln->sl[i]] = 0; in read_alignment_clustal() 1572 aln->seq[i][aln->sl[i]] = 0; in read_alignment_clustal() 1656 aln->sl[i-1] = aln->sl[i]; in read_sequences() 1698 aln->s[i][aln->sl[i]] = 0; in read_sequences() 1699 aln->seq[i][aln->sl[i]] = 0; in read_sequences() 1700 aln->sn[i][aln->lsn[i]] = 0; in read_sequences() 1786 aln->sl[i-1] = aln->sl[i]; in read_alignment() [all …]
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H A D | kalign2_output.c | 88 if(aln->ft){ in macsim_output() 110 tmp =aln->s[f][aln->sl[f]]; in macsim_output() 162 tmp =aln->s[i][aln->sl[i]]; in msf_output() 307 tmp =aln->s[i][aln->sl[i]]; in clustal_output() 445 tmp =aln->s[i][aln->sl[i]]; in aln_output() 548 min_len = (aln->lsn[i] < aln->lsn[j])? aln->lsn[i] : aln->lsn[j]; in get_meaningful_names() 552 if( aln->sn[i][c] != aln->sn[j][c]){ in get_meaningful_names() 556 if(aln->sn[i][c] == aln->sn[j][c]){ in get_meaningful_names() 557 if(aln->sn[i][c] != '_' && aln->sn[i][c] != '-'){ in get_meaningful_names() 576 if(!isalnum((int)aln->sn[i][j]) && aln->sn[i][j] != '_' && aln->sn[i][j] != '-'){ in get_meaningful_names() [all …]
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H A D | kalign2_misc.c | 170 aln = sort_in_relation(aln,sort); in sort_sequences() 183 return aln; in sort_sequences() 238 return aln; in sort_in_relation() 259 aln->sip[left][0] = aln->sip[right][0]; in q_sort() 260 aln->nsip[left] = aln->nsip[right]; in q_sort() 267 aln->sip[right][0] = aln->sip[left][0]; in q_sort() 268 aln->nsip[right] = aln->nsip[left]; in q_sort() 346 return aln; in make_dna() 636 update_gaps(aln->sl[aln->sip[a][i]],aln->s[aln->sip[a][i]],path[0],gap_a); in make_seq() 639 update_gaps(aln->sl[aln->sip[b][i]],aln->s[aln->sip[b][i]],path[0],gap_b); in make_seq() [all …]
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H A D | kalign2_main.c | 64 aln = detect_and_read_sequences(aln,param); in _main() 73 param->dna = byg_detect(aln->s[i],aln->sl[i]); in _main() 88 free_aln(aln); in _main() 92 aln = make_dna(aln); in _main() 97 aln->nsip[i] = i; in _main() 99 aln->s[i][j] = 0; in _main() 103 output(aln,param); in _main() 202 ntree_data->aln = aln; in _main() 263 p = aln->s[i]; in _main() 273 aln = make_seq(aln,a,b,map[tree[i+2]]); in _main() [all …]
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H A D | kalign2_mem.c | 142 return aln; in aln_alloc() 157 if(aln->ft){ in free_aln() 161 free(aln->ft); in free_aln() 163 if(aln->si){ in free_aln() 164 free(aln->si); in free_aln() 172 free(aln->seq); in free_aln() 173 free(aln->s); in free_aln() 174 free(aln->sn); in free_aln() 175 free(aln->sl); in free_aln() 176 free(aln->lsn); in free_aln() [all …]
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H A D | kalign2_alignment_types.c | 68 len_a = aln->sl[a]; in default_alignment() 69 len_b = aln->sl[b]; in default_alignment() 85 set_gap_penalties(profile[a],len_a,aln->nsip[b],0,aln->nsip[a]); in default_alignment() 86 set_gap_penalties(profile[b],len_b,aln->nsip[a],0,aln->nsip[b]); in default_alignment() 91 map[c] = ps_dyn(map[c],dp,profb,aln->s[a],len_b,len_a,aln->nsip[b]); in default_alignment() 96 map[c] = ps_dyn(map[c],dp,profa,aln->s[b],len_a,len_b,aln->nsip[a]); in default_alignment() 114 aln->nsip[c] = aln->nsip[a] + aln->nsip[b]; in default_alignment() 115 aln->sip[c] = malloc(sizeof(int)*(aln->nsip[a] + aln->nsip[b])); in default_alignment() 118 aln->sip[c][g] = aln->sip[a][j]; in default_alignment() 122 aln->sip[c][g] = aln->sip[b][j]; in default_alignment() [all …]
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H A D | kalign2_profile_alignment.c | 63 aln->s[i] = assign_gap_codes(aln->s[i],aln->sl[i]); in profile_alignment_main() 121 p = aln->s[i]; in profile_alignment_main() 132 aln = make_seq(aln,a,b,map[c]); in profile_alignment_main() 138 aln = sort_sequences(aln,tree,param->sort); in profile_alignment_main() 252 aln->nsip[c] = aln->nsip[a] + aln->nsip[b]; in hirschberg_profile_alignment() 253 aln->sip[c] = malloc(sizeof(int)*(aln->nsip[a] + aln->nsip[b])); in hirschberg_profile_alignment() 256 aln->sip[c][g] = aln->sip[a][j]; in hirschberg_profile_alignment() 260 aln->sip[c][g] = aln->sip[b][j]; in hirschberg_profile_alignment() 337 seq = aln->s[aln->sip[num][a]]; in make_profile_from_alignment() 408 p = aln->s[i]; in protein_profile_wu_distance() [all …]
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/dports/biology/p5-Bio-Phylo/Bio-Phylo-v2.0.1/t/ |
H A D | 24-bioperl-alignio.t | 348 while ( $aln = <$in> ) { 349 $aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl($aln); 409 $aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln($aln) ); 730 is( $aln->is_flush, 1 ); 742 $aln->unmatch(); 776 $aln = 873 is $aln->length, 25; 875 is $aln->no_sequences, 4; 890 is $aln->length, 20; 966 $aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl($aln); [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/AlignIO/ |
H A D | emboss.t | 21 $aln = $str->next_aln(); 23 is($aln->score,'501.50'); 30 is($aln->length,364); 36 $aln = $str->next_aln(); 38 is($aln->score,'499.50'); 46 $aln = $str->next_aln(); 51 $aln = $str->next_aln(); 61 $aln = $str->next_aln(); 63 is($aln->score,'18.0'); 67 is($aln->length,238); [all …]
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H A D | nexus.t | 23 $aln = $str->next_aln(); 35 $aln = $str->next_aln(); 41 $aln = $str->next_aln(); 47 $aln = $str->next_aln(); 53 $aln = $str->next_aln(); 59 $aln = $str->next_aln(); 65 $aln = $str->next_aln(); 71 $aln = $str->next_aln(); 77 $aln = $str->next_aln(); 83 $aln = $str->next_aln(); [all …]
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H A D | arp.t | 17 my ($str,$aln,$strout,$status); 25 $aln = $str->next_aln(); 26 isa_ok($aln,'Bio::Align::AlignI'); 32 my $coll = $aln->annotation; 46 $aln = $str->next_aln(); 47 isa_ok($aln,'Bio::Align::AlignI'); 52 $coll = $aln->annotation; 62 $aln = $str->next_aln(); 68 $coll = $aln->annotation; 78 $aln = $str->next_aln(); [all …]
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H A D | meme.t | 21 my $aln = $str->next_aln(); 22 isa_ok($aln,'Bio::Align::AlignI');is $aln->length,25; 23 is $aln->num_sequences,4; 25 is $aln->get_seq_by_pos(3)->strand,"1"; 32 $aln = $str->next_aln(); 33 isa_ok($aln,'Bio::Align::AlignI');is $aln->length,20; 34 is $aln->num_sequences,8; 37 is $aln->get_seq_by_pos(6)->strand,"1"; 44 $aln = $str->next_aln(); 45 isa_ok($aln,'Bio::Align::AlignI');is $aln->length,21; [all …]
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H A D | phylip.t | 15 my ($str,$aln,$strout,$status); 20 $aln = $strout->next_aln($aln); 21 isa_ok($aln,'Bio::Align::AlignI'); 34 $aln = $str->next_aln(); 36 isa_ok($aln,'Bio::Align::AlignI'); 45 $aln = $str->next_aln(); 55 $aln = $str->next_aln(); 82 $aln = $str->next_aln(); 83 $ls = $aln->get_seq_by_pos(9); 90 $aln = $io->next_aln(); [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
H A D | best_placement.cpp | 263 if(!aln.GetSegs().IsSpliced()) { in GetLongestMatchrunLen() 323 _ASSERT(isProtSS(aln)); in s_GetIdentOdds_protSS() 366 _ASSERT(aln.GetSegs().IsSpliced() && !isProtSS(aln)); in s_GetIdentOdds_nucSS() 397 if(isProtSS(aln)) { in GetIdentOdds() 444 if(aln.GetSegs().IsSpliced() && !isProtSS(aln)) { in GetIdentOdds() 450 cerr << MSerial_AsnText << aln; in GetIdentOdds() 603 return get_score(aln); in GetScore() 619 for(const auto aln : sas.Set()) { in Rank() local 624 v.emplace_back(score_fn(*aln), aln); in Rank() 642 auto aln = p.second; in Rank() local [all …]
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/ |
H A D | KalignAdapter.cpp | 129 aln = aln_alloc(aln); in alignUnsafe() 158 aln->s[i][j] = aacode[toupper(aln->seq[i][j]) - 65]; in alignUnsafe() 163 aln->s[i][aln->sl[i]] = 0; in alignUnsafe() 164 aln->seq[i][aln->sl[i]] = 0; in alignUnsafe() 165 aln->sn[i][aln->lsn[i]] = 0; in alignUnsafe() 184 param->dna = byg_detect(aln->s[i], aln->sl[i]); in alignUnsafe() 204 aln = make_dna(aln); in alignUnsafe() 390 aln = make_seq(aln, a, b, map[tree[i + 2]]); in alignUnsafe() 401 aln = sort_sequences(aln, tree, param->sort); in alignUnsafe() 415 seq += QString(aln->s[f][j], '-') + aln->seq[f][j]; in alignUnsafe() [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Align/ |
H A D | PairwiseStatistics.pm | 101 my ($self,$aln) = @_; 102 if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { 110 my $L = $aln->length - $self->number_of_gaps($aln); 126 my ($self,$aln) = @_; 127 if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { 135 foreach my $seq ( $aln->each_seq ) { 165 my ($self,$aln) = @_; 166 if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { 173 my $gapline = $aln->gap_line; 208 if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) { [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/io/ |
H A D | file_formats_msa.c | 179 aln = NULL; in vrna_file_msa_detect_format() 254 if (names && aln) { in vrna_file_msa_read() 256 *aln = NULL; in vrna_file_msa_read() 350 *aln = NULL; in vrna_file_msa_read_record() 523 *aln = NULL; in parse_stockholm_alignment() 891 (*aln)[nn] = (char *)vrna_realloc((*aln)[nn], in parse_clustal_alignment() 946 *aln = NULL; in parse_maf_alignment() 1041 if (aln && (*aln)) in free_msa_record() 1064 if (aln && (*aln)) { in free_msa_record() 1065 free(*aln); in free_msa_record() [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/AlignIO/ |
H A D | mega.pm | 139 $aln->match_char($value); 141 $aln->gap_char($value); 172 $aln->add_seq($seq); 174 $aln->unmatch; 175 return $aln if $aln->num_sequences; 190 my ($self,@aln) = @_; 195 foreach my $aln ( @aln ) { 196 if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { 203 $aln->match(); 207 $aln->match_char, $aln->gap_char); [all …]
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H A D | nexus.pm | 210 $aln->gap_char($gap); 320 $aln->add_seq($seq); 336 return $aln if $aln->num_sequences; 369 my ($self,@aln) = @_; 376 foreach my $aln (@aln) { 377 if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) { 384 $length = $aln->length(); 387 $aln->id, $aln->num_sequences, $length)); 388 $match = "match=". $aln->match_char if $aln->match_char; 389 $missing = "missing=". $aln->missing_char if $aln->missing_char; [all …]
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/dports/biology/fasta3/fasta-36.3.8/src/ |
H A D | c_dispn.c | 118 ioff0=aln->smin0; in discons() 120 ioff1=aln->smin1; in discons() 159 aln->q_offset+qlsgn*ioff0*aln->llmult+qfx0); in discons() 224 aln->q_offset+qlsgn*(ioff0-del0)*aln->llmult+qfx0, in discons() 261 if (qlsgn > 0) {q_digit_max = aln->smin0 + (aln->amax0 - aln->amin0); } in discons() 265 if (llsgn > 0) {s_digit_max = aln->smin1 + (aln->amax1 - aln->amin1); } in discons() 267 s_digit_max = aln->l_offset + aln->frame + llsgn*aln->llmult*s_digit_max + 1l; in discons() 569 aln->d_start0 = q_offset+q_lsgn*aln->amin0+q_fx0; in calc_coord() 570 aln->d_stop0 = q_offset+q_lsgn*aln->amax0+q_fxn; in calc_coord() 571 aln->d_start1 = l_offset+l_lsgn*aln->amin1*aln->llmult+l_fx0; in calc_coord() [all …]
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H A D | cal_consf.c | 148 …n0t=lenc=len_gap=aln->nident=aln->nmismatch=aln->nsim=aln->npos=aln->ngap_q=aln->ngap_l=op=p_ac= 0; in calc_cons_a() 241 if (itmp>aln->llen/2) ns += aln->llen; in calc_cons_a() 378 …lenc = len_gap =aln->nident=aln->nmismatch=aln->nsim=aln->npos=aln->ngap_q=aln->ngap_l=aln->nfs=op… in calc_code() 414 aln->npos++; in calc_code() 415 aln->nsim++; in calc_code() 419 aln->nsim++; in calc_code() 450 aln->q_offset+i0+1,aln->l_offset+i1+1, in calc_code() 545 …lenc=len_gap=aln->nident=aln->nmismatch=aln->nsim=aln->npos=aln->ngap_q = aln->ngap_l = aln->nfs =… in calc_id() 554 aln->nsim++; in calc_id() 555 aln->npos++; in calc_id() [all …]
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H A D | cal_cons.c | 127 struct a_struct *aln, in calc_cons_a() argument 204 if (min(a_res->min0,a_res->min1)<aln->llen || aln->showall==1) in calc_cons_a() 214 aln->smin1 = 0; in calc_cons_a() 230 aln->smin0 = 0; in calc_cons_a() 270 lenc = aln->nident = aln->nmismatch = in calc_cons_a() 271 aln->npos = aln->nsim = aln->ngap_q = aln->ngap_l = aln->nfs = op = 0; in calc_cons_a() 457 aln->ngap_q++; in calc_cons_a() 496 aln->ngap_l++; in calc_cons_a() 536 if (itmp>aln->llen/2) ns += aln->llen; /* more than 1/2 , use another*/ in calc_cons_a() 812 …lenc = aln->nident = aln->nmismatch = aln->nsim = aln->npos = aln->ngap_q = aln->ngap_l = aln->nfs… in calc_code() [all …]
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/dports/biology/vt/vt-0.57721/lib/htslib/test/ |
H A D | sam.c | 117 bam1_t *aln = bam_init1(); in aux_fields1() local 139 bam_aux_del(aln,p); in aux_fields1() 140 if (bam_aux_get(aln,"XA")) in aux_fields1() 168 check_int_B_array(aln, "B0", in aux_fields1() 170 check_int_B_array(aln, "B1", in aux_fields1() 172 check_int_B_array(aln, "B2", in aux_fields1() 174 check_int_B_array(aln, "B3", in aux_fields1() 176 check_int_B_array(aln, "B4", in aux_fields1() 246 bam_destroy1(aln); in aux_fields1() 264 bam1_t *aln = bam_init1(); in copy_check_alignment() local [all …]
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/test/ |
H A D | sam.c | 117 bam1_t *aln = bam_init1(); in aux_fields1() local 139 bam_aux_del(aln,p); in aux_fields1() 140 if (bam_aux_get(aln,"XA")) in aux_fields1() 168 check_int_B_array(aln, "B0", in aux_fields1() 170 check_int_B_array(aln, "B1", in aux_fields1() 172 check_int_B_array(aln, "B2", in aux_fields1() 174 check_int_B_array(aln, "B3", in aux_fields1() 176 check_int_B_array(aln, "B4", in aux_fields1() 246 bam_destroy1(aln); in aux_fields1() 264 bam1_t *aln = bam_init1(); in copy_check_alignment() local [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Align/ |
H A D | AlignStats.t | 20 my $aln = $in->next_aln(); 21 isa_ok($aln, 'Bio::Align::AlignI'); 23 is( $stats->transversions($aln),4); 24 is( $stats->transitions($aln),9); 29 is( $stats->pairwise_stats->score_nuc( -aln => $aln, -match => 1, 36 $d = $stats->distance(-align=> $aln, 59 $aln = $in->next_aln(); 60 isa_ok($aln,'Bio::Align::AlignI'); 63 is( $stats->transitions($aln),17); 68 is( $stats->pairwise_stats->score_nuc( -aln => $aln, -match => 1, [all …]
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