Lines Matching refs:pairarray
555 …struct Pair_T *pairarray; /* The array version of pairs_fwd or pairs_rev, with the gaps substitute… member
677 return this->pairarray; in Stage3_pairarray()
704 return Pair_querypos(&(this->pairarray[0])); in Stage3_querystart()
709 return Pair_querypos(&(this->pairarray[this->npairs-1])); in Stage3_queryend()
786 return Pair_genomepos(&(this->pairarray[0])); in Stage3_chrstart()
791 return Pair_genomepos(&(this->pairarray[this->npairs-1])); in Stage3_chrend()
834 querystart = Pair_querypos(&(this->pairarray[0])); in Stage3_domain()
835 queryend = Pair_querypos(&(this->pairarray[this->npairs-1])); in Stage3_domain()
846 querystart = Pair_querypos(&(this->pairarray[0])); in Stage3_largemargin()
847 queryend = Pair_querypos(&(this->pairarray[this->npairs-1])); in Stage3_largemargin()
881 return this->chroffset + Pair_genomicpos(this->pairarray,this->npairs,querypos,headp); in Stage3_genomicpos()
893 querystart = Pair_querypos(&(part1->pairarray[0])); in Stage3_chimeric_goodness()
897 part1->pairarray,part1->npairs,part1->cdna_direction, in Stage3_chimeric_goodness()
903 queryend = Pair_querypos(&(part2->pairarray[part2->npairs-1])); in Stage3_chimeric_goodness()
907 part2->pairarray,part2->npairs,part2->cdna_direction, in Stage3_chimeric_goodness()
1038 querypos1 = Pair_querypos(&(x->pairarray[0])); in Stage3_position_cmp()
1039 querypos2 = Pair_querypos(&(y->pairarray[0])); in Stage3_position_cmp()
1045 querypos1 = Pair_querypos(&(x->pairarray[x->npairs-1])); in Stage3_position_cmp()
1046 querypos2 = Pair_querypos(&(y->pairarray[y->npairs-1])); in Stage3_position_cmp()
1064 x_querystart = Pair_querypos(&(x->pairarray[0])); in Stage3_querystart_cmp()
1065 y_querystart = Pair_querypos(&(y->pairarray[0])); in Stage3_querystart_cmp()
1082 x_queryend = Pair_querypos(&(x->pairarray[x->npairs-1])); in Stage3_queryend_cmp()
1083 y_queryend = Pair_querypos(&(y->pairarray[y->npairs-1])); in Stage3_queryend_cmp()
1120 x_querystart = Pair_querypos(&(x->pairarray[0])); in Stage3_chrnum_querystart_cmp()
1121 y_querystart = Pair_querypos(&(y->pairarray[0])); in Stage3_chrnum_querystart_cmp()
1129 x_length = Pair_querypos(&(x->pairarray[x->npairs-1])) - x_querystart; in Stage3_chrnum_querystart_cmp()
1130 y_length = Pair_querypos(&(y->pairarray[y->npairs-1])) - y_querystart; in Stage3_chrnum_querystart_cmp()
1154 x_queryend = Pair_querypos(&(x->pairarray[x->npairs-1])); in Stage3_chrnum_queryend_cmp()
1155 y_queryend = Pair_querypos(&(y->pairarray[y->npairs-1])); in Stage3_chrnum_queryend_cmp()
1163 x_length = x_queryend - Pair_querypos(&(x->pairarray[0])); in Stage3_chrnum_queryend_cmp()
1164 y_length = y_queryend - Pair_querypos(&(y->pairarray[0])); in Stage3_chrnum_queryend_cmp()
5223 FREE_OUT((*old)->pairarray); in Stage3_free_pairarray()
5227 FREE_OUT((*old)->pairarray); in Stage3_free_pairarray()
5240 struct Pair_T *pairarray; in make_pairarray() local
5282 newpair = pairarray = (struct Pair_T *) MALLOC_OUT(*npairs*sizeof(struct Pair_T)); in make_pairarray()
5289 Pair_set_genomepos(pairarray,*npairs,chroffset,chrhigh,watsonp); in make_pairarray()
5291 return pairarray; in make_pairarray()
5303 struct Pair_T *pairarray, *pairarray_save; in make_pairarray_merge() local
5309 pairarray_save = this_left->pairarray; in make_pairarray_merge()
5329 this_left->pairarray = pairarray_save; in make_pairarray_merge()
5359 newpair = pairarray = (struct Pair_T *) MALLOC_OUT(this_left->npairs*sizeof(struct Pair_T)); in make_pairarray_merge()
5366 Pair_set_genomepos(pairarray,this_left->npairs,chroffset,chrhigh,watsonp); in make_pairarray_merge()
5367 this_left->pairarray = pairarray; in make_pairarray_merge()
5374 &min_splice_prob,this_left->pairarray,this_left->npairs,this_left->cdna_direction); in make_pairarray_merge()
5426 this_left->pairarray = (struct Pair_T *) NULL; in make_pairarrays_chimera()
5427 this_right->pairarray = (struct Pair_T *) NULL; in make_pairarrays_chimera()
5433 …newpair = this_left->pairarray = (struct Pair_T *) MALLOC_OUT((newnpairs + gaplength)*sizeof(struc… in make_pairarrays_chimera()
5440 … Pair_set_genomepos(this_left->pairarray,this_left->npairs,this_left->chroffset,this_left->chrhigh, in make_pairarrays_chimera()
5446 &min_splice_prob,this_left->pairarray,this_left->npairs,this_left->cdna_direction); in make_pairarrays_chimera()
5449 newpair = this_right->pairarray = &(this_left->pairarray[this_left->npairs + gaplength]); in make_pairarrays_chimera()
5456 …Pair_set_genomepos(this_right->pairarray,this_right->npairs,this_right->chroffset,this_right->chrh… in make_pairarrays_chimera()
5462 &min_splice_prob,this_right->pairarray,this_right->npairs,this_right->cdna_direction); in make_pairarrays_chimera()
5556 start = &(stage3->pairarray[0]); in Stage3_recompute_coverage()
5557 end = &(stage3->pairarray[stage3->npairs - 1]); in Stage3_recompute_coverage()
5899 Stage3_new (struct Pair_T *pairarray, List_T pairs, int npairs, int goodness, int cdna_direction, i… in Stage3_new() argument
5920 start = &(pairarray[0]); in Stage3_new()
5921 end = &(pairarray[npairs-1]); in Stage3_new()
5928 …cigar_tokens = Pair_compute_cigar(&intronp,&hardclip_start,&hardclip_end,pairarray,npairs,querylen… in Stage3_new()
5933 Pair_dump_array_stderr(pairarray,npairs,/*zerobasedp*/true); in Stage3_new()
5947 new->pairarray = pairarray; in Stage3_new()
5972 …new->cdna_direction = Pair_guess_cdna_direction_array(&new->sensedir,pairarray,npairs,/*invertedp*… in Stage3_new()
6007 new->circularpos = Pair_circularpos(&alias,pairarray,npairs,chrlength,watsonp,querylength); in Stage3_new()
6049 struct Pair_T *pairarray; in Stage3_new_from_pairs() local
6059 pairarray = make_pairarray(&npairs,&pairs,cdna_direction,watsonp, in Stage3_new_from_pairs()
6067 &min_splice_prob,pairarray,npairs,cdna_direction); in Stage3_new_from_pairs()
6069 return Stage3_new(pairarray,pairs,npairs,goodness,cdna_direction,sensedir, in Stage3_new_from_pairs()
6130 new->pairarray = (struct Pair_T *) MALLOC_OUT(old->npairs*sizeof(struct Pair_T));
6131 memcpy(new->pairarray,old->pairarray,old->npairs*sizeof(struct Pair_T));
6188 FREE_OUT((*old)->pairarray); in Stage3_free()
6223 this->pairarray,this->npairs,Sequence_fullpointer(queryaaseq),strictp); in Stage3_translate_cdna()
6229 Backtranslation_cdna(this->pairarray,this->npairs,this->translation_start,this->translation_end); in Stage3_backtranslate_cdna()
6246 this->pairarray,this->npairs,/*backwardsp*/true,/*revcompp*/true,/*fulllengthp*/true, in truncate_fulllength()
6251 this->pairarray,this->npairs,/*backwardsp*/false,/*revcompp*/false,/*fulllengthp*/true, in truncate_fulllength()
6256 this->npairs = Pair_clip_bounded_array(this->pairarray,this->npairs, in truncate_fulllength()
6269 this->pairarray,npairs,/*backwardsp*/true,/*revcompp*/true,fulllengthp, in Stage3_translate_genomic()
6274 this->pairarray,npairs,/*backwardsp*/false,/*revcompp*/false,fulllengthp, in Stage3_translate_genomic()
6282 this->pairarray,npairs,/*backwardsp*/true,/*revcompp*/true,fulllengthp, in Stage3_translate_genomic()
6287 this->pairarray,npairs,/*backwardsp*/false,/*revcompp*/false,fulllengthp, in Stage3_translate_genomic()
6307 this->pairarray,this->npairs,this->watsonp,/*backwardsp*/true,/*revcompp*/true,
6308 reference->pairarray,reference->npairs,reference->watsonp);
6311 this->pairarray,this->npairs,this->watsonp,/*backwardsp*/false,/*revcompp*/false,
6312 reference->pairarray,reference->npairs,reference->watsonp);
6317 this->pairarray,this->npairs,this->watsonp,/*backwardsp*/false,/*revcompp*/false,
6318 reference->pairarray,reference->npairs,reference->watsonp);
6321 this->pairarray,this->npairs,this->watsonp,/*backwardsp*/true,/*revcompp*/true,
6322 reference->pairarray,reference->npairs,reference->watsonp);
6369 this->pairarray,this->npairs,Sequence_fullpointer(queryseq),strictp); in Stage3_translate()
6370 Backtranslation_cdna(this->pairarray,this->npairs,this->translation_start,this->translation_end); in Stage3_translate()
6375 this->pairarray,this->npairs,/*backwardsp*/true,/*revcompp*/true,fulllengthp, in Stage3_translate()
6380 this->pairarray,this->npairs,/*backwardsp*/false,/*revcompp*/false,fulllengthp, in Stage3_translate()
6389 this->pairarray,this->npairs,/*backwardsp*/true,/*revcompp*/true,fulllengthp, in Stage3_translate()
6394 this->pairarray,this->npairs,/*backwardsp*/false,/*revcompp*/false,fulllengthp, in Stage3_translate()
6422 this->pairarray,npairs1 + npairs2,Sequence_fullpointer(queryseq),strictp); in Stage3_translate_chimera()
6423 Backtranslation_cdna(this->pairarray,npairs1 + npairs2,translation_start,translation_end); in Stage3_translate_chimera()
6428 this->pairarray,npairs1 + npairs2,/*backwardsp*/true,/*revcompp*/true,fulllengthp, in Stage3_translate_chimera()
6433 this->pairarray,npairs1 + npairs2,/*backwardsp*/false,/*revcompp*/false,fulllengthp, in Stage3_translate_chimera()
6442 this->pairarray,npairs1 + npairs2,/*backwardsp*/true,/*revcompp*/true,fulllengthp, in Stage3_translate_chimera()
6447 this->pairarray,npairs1 + npairs2,/*backwardsp*/false,/*revcompp*/false,fulllengthp, in Stage3_translate_chimera()
6488 this->translation_length = Pair_translation_length(this->pairarray,this->npairs); in Stage3_translate_chimera()
6489 mate->translation_length = Pair_translation_length(mate->pairarray,mate->npairs); in Stage3_translate_chimera()
6493 this->relaastart = this->pairarray[this->translation_start].aapos; in Stage3_translate_chimera()
6494 this->relaaend = this->pairarray[this->translation_end].aapos; in Stage3_translate_chimera()
6496 mate->relaastart = mate->pairarray[mate->translation_start].aapos; in Stage3_translate_chimera()
6497 mate->relaaend = mate->pairarray[mate->translation_end].aapos; in Stage3_translate_chimera()
6512 start = &(this->pairarray[0]); in Stage3_print_pathsummary()
6513 end = &(this->pairarray[this->npairs-1]); in Stage3_print_pathsummary()
6519 Pair_nexons(this->pairarray,this->npairs),this->matches,this->unknowns,this->mismatches, in Stage3_print_pathsummary()
6524 Translation_print_comparison(fp,this->pairarray,this->npairs,this->relaastart,this->relaaend); in Stage3_print_pathsummary()
6536 start = &(this->pairarray[0]); in Stage3_print_pslformat_nt()
6537 end = &(this->pairarray[this->npairs-1]); in Stage3_print_pslformat_nt()
6539 Pair_print_pslformat_nt(fp,this->pairarray,this->npairs,start,end,queryaaseq,this->chrnum, in Stage3_print_pslformat_nt()
6557 start = &(this->pairarray[0]); in Stage3_print_pslformat_pro()
6558 end = &(this->pairarray[this->npairs-1]); in Stage3_print_pslformat_pro()
6560 Pair_print_pslformat_pro(fp,this->pairarray,this->npairs,start,end,queryaaseq,this->chrnum, in Stage3_print_pslformat_pro()
6590 start = &(this->pairarray[0]); in Stage3_print_gff3()
6591 end = &(this->pairarray[this->npairs-1]); in Stage3_print_gff3()
6601 Pair_print_gff3(fp,this->pairarray,this->npairs,pathnum, in Stage3_print_gff3()
6620 Pair_print_bedpe(fp,this->pairarray,this->npairs,this->chrnum,this->watsonp,chromosome_iit); in Stage3_print_bedpe()
6642 pair = &(this->pairarray[0]); in Stage3_print_sam()
6645 pair = &(this->pairarray[this->npairs-1]); in Stage3_print_sam()
6650 Pair_print_sam(fp,abbrev,this->pairarray,this->npairs, in Stage3_print_sam()
6658 Pair_print_sam(fp,abbrev,this->pairarray,this->npairs, in Stage3_print_sam()
6667 Pair_print_sam(fp,abbrev,this->pairarray,this->npairs, in Stage3_print_sam()
6687 start = &(this->pairarray[0]); in Stage3_print_iit_map()
6688 end = &(this->pairarray[this->npairs-1]); in Stage3_print_iit_map()
6699 start = &(this->pairarray[0]); in Stage3_print_iit_exon_map()
6700 end = &(this->pairarray[this->npairs-1]); in Stage3_print_iit_exon_map()
6702 Pair_print_iit_exon_map(fp,this->pairarray,this->npairs,queryseq,Sequence_accession(queryseq), in Stage3_print_iit_exon_map()
6709 Pair_print_splicesites(fp,this->pairarray,this->npairs,Sequence_accession(queryseq), in Stage3_print_splicesites()
6710 Pair_nexons(this->pairarray,this->npairs),this->chrnum, in Stage3_print_splicesites()
6717 Pair_print_introns(fp,this->pairarray,this->npairs,Sequence_accession(queryseq), in Stage3_print_introns()
6718 Pair_nexons(this->pairarray,this->npairs),this->chrnum, in Stage3_print_introns()
6733 start = &(this->pairarray[0]);
6734 end = &(this->pairarray[this->npairs-1]);
6743 Pair_nexons(this->pairarray,this->npairs),this->matches,this->unknowns,this->mismatches,
6746 Translation_print_comparison(fp,this->pairarray,this->npairs,this->relaastart,this->relaaend);
6750 Pair_print_alignment(fp,this->pairarray,this->npairs,reference->chrnum,reference->chroffset,
6753 debug1(Pair_dump_array(this->pairarray,this->npairs,/*zerobasedp*/true));
6754 debug1(Pair_check_array(this->pairarray,this->npairs));
6781 start = &(this->pairarray[0]); in print_map()
6782 end = &(this->pairarray[this->npairs-1]); in print_map()
6873 exonbounds = Pair_exonbounds(this->pairarray,this->npairs); in print_exon_map()
6931 Pair_print_exonsummary(fp,this->pairarray,this->npairs,this->chrnum,this->chroffset, in Stage3_print_alignment()
6933 Pair_print_continuous_byexon(fp,this->pairarray,this->npairs,this->watsonp,invertmode); in Stage3_print_alignment()
6936 Pair_print_continuous(fp,this->pairarray,this->npairs,this->watsonp, in Stage3_print_alignment()
6940 Pair_print_exonsummary(fp,this->pairarray,this->npairs,this->chrnum,this->chroffset, in Stage3_print_alignment()
6943 Pair_print_alignment(fp,this->pairarray,this->npairs,this->chrnum,this->chroffset, in Stage3_print_alignment()
6947 debug1(Pair_dump_array(this->pairarray,this->npairs,/*zerobasedp*/true)); in Stage3_print_alignment()
6948 debug1(Pair_check_array(this->pairarray,this->npairs)); in Stage3_print_alignment()
6955 Pair_print_coordinates(fp,this->pairarray,this->npairs,this->chrnum,this->chroffset, in Stage3_print_coordinates()
6964 Pair_print_nucleotide_cdna(fp,this->pairarray,this->npairs,wraplength); in Stage3_print_cdna()
6967 Pair_print_protein_cdna(fp,this->pairarray,this->npairs,wraplength,/*forwardp*/true); in Stage3_print_cdna()
6969 …Pair_print_protein_cdna(fp,&(this->pairarray[this->npairs-1]),this->npairs,wraplength,/*forwardp*/… in Stage3_print_cdna()
6978 Pair_print_protein_genomic(fp,this->pairarray,this->npairs,wraplength,/*forwardp*/true); in Stage3_print_protein_genomic()
6980 …Pair_print_protein_genomic(fp,&(this->pairarray[this->npairs-1]),this->npairs,wraplength,/*forward… in Stage3_print_protein_genomic()
7005 start = &(this->pairarray[0]); in Stage3_print_compressed()
7006 end = &(this->pairarray[this->npairs-1]); in Stage3_print_compressed()
7008 Pair_nexons(this->pairarray,this->npairs), in Stage3_print_compressed()
7009 Stage3_fracidentity(this),this->pairarray,this->npairs, in Stage3_print_compressed()
12923 Stage3_short_alignment_p (struct Pair_T *pairarray, int npairs, int querylength) { in Stage3_short_alignment_p() argument
12929 querystart = pairarray[0].querypos; in Stage3_short_alignment_p()
12930 queryend = pairarray[npairs-1].querypos; in Stage3_short_alignment_p()
12944 Stage3_bad_stretch_p (struct Pair_T *pairarray, int npairs, int pos5, int pos3) {
12960 pair = &(pairarray[i]);
13076 Stage3_bad_stretch_p (struct Pair_T *pairarray, int npairs, int pos5, int pos3) { in Stage3_bad_stretch_p() argument
13085 ptr = pairarray; in Stage3_bad_stretch_p()
13140 Stage3_good_part (struct Pair_T *pairarray, int npairs, int pos5, int pos3) { in Stage3_good_part() argument
13159 pair = &(pairarray[i]); in Stage3_good_part()
13284 pair = &(pairarray[i]); in Stage3_good_part()
17913 this->pairarray = make_pairarray(&this->npairs,&this->pairs,this->cdna_direction, in Stage3_extend_right()
17919 &min_splice_prob,this->pairarray,this->npairs,this->cdna_direction); in Stage3_extend_right()
17921 if (this->pairarray == NULL) { in Stage3_extend_right()
18110 this->pairarray = make_pairarray(&this->npairs,&this->pairs,this->cdna_direction, in Stage3_extend_left()
18116 &min_splice_prob,this->pairarray,this->npairs,this->cdna_direction); in Stage3_extend_left()
18118 if (this->pairarray == NULL) { in Stage3_extend_left()
18155 this->pairarray = make_pairarray(&this->npairs,&this->pairs,this->cdna_direction, in Stage3_trim_right()
18161 &min_splice_prob,this->pairarray,this->npairs,this->cdna_direction); in Stage3_trim_right()
18163 if (this->pairarray == NULL) { in Stage3_trim_right()
18203 this->pairarray = make_pairarray(&this->npairs,&this->pairs,this->cdna_direction, in Stage3_trim_left()
18209 &min_splice_prob,this->pairarray,this->npairs,this->cdna_direction); in Stage3_trim_left()
18211 if (this->pairarray == NULL) { in Stage3_trim_left()
18273 this_left->pairarray = (struct Pair_T *) NULL; in merge_local_single()
18274 this_right->pairarray = (struct Pair_T *) NULL; in merge_local_single()
18410 …this_left->pairarray = make_pairarray(&this_left->npairs,&this_left->pairs,this_left->cdna_directi… in merge_local_single()
18416 &min_splice_prob,this_left->pairarray,this_left->npairs,this_left->cdna_direction); in merge_local_single()
18419 …this_right->pairarray = make_pairarray(&this_right->npairs,&this_right->pairs,this_right->cdna_dir… in merge_local_single()
18425 &min_splice_prob,this_right->pairarray,this_right->npairs,this_right->cdna_direction); in merge_local_single()
18853 struct Pair_T *pairarray; in Stage3_split() local
18902 pairarray = make_pairarray(&npairs,&pairs,this->cdna_direction,this->watsonp, in Stage3_split()
18911 &min_splice_prob,pairarray,npairs,this->cdna_direction); in Stage3_split()
18913 if ((stage3 = Stage3_new(pairarray,pairs,npairs,goodness,this->cdna_direction,this->sensedir, in Stage3_split()
18933 pairarray = make_pairarray(&npairs,&pairs,this->cdna_direction,this->watsonp, in Stage3_split()
18942 &min_splice_prob,pairarray,npairs,this->cdna_direction); in Stage3_split()
18944 if ((stage3 = Stage3_new(pairarray,pairs,npairs,goodness,this->cdna_direction,this->sensedir, in Stage3_split()
18964 …this->cdna_direction = Pair_guess_cdna_direction_array(&this->sensedir,this->pairarray,this->npair… in Stage3_guess_cdna_direction()
18966 Pair_fix_cdna_direction_array(this->pairarray,this->npairs,this->cdna_direction); in Stage3_guess_cdna_direction()