Searched refs:ACCEPTOR_MODEL_LEFT_MARGIN (Results 1 – 8 of 8) sorted by relevance
/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | maxent.c | 99341 i = nucleotides[ACCEPTOR_MODEL_LEFT_MARGIN - 2]*4 + nucleotides[ACCEPTOR_MODEL_LEFT_MARGIN - 1]; in score_acceptor_dinucleotide_nucleotides() 99439 if (sequence_okay(sequence,ACCEPTOR_MODEL_LEFT_MARGIN+ACCEPTOR_MODEL_RIGHT_MARGIN) == false) { in Maxent_acceptor_prob() 99454 odds = score_acceptor_dinucleotide(sequence[ACCEPTOR_MODEL_LEFT_MARGIN-2], in Maxent_acceptor_prob() 99455 sequence[ACCEPTOR_MODEL_LEFT_MARGIN-1])*maxentscore; in Maxent_acceptor_prob() 99466 if (sequence_okay(sequence,ACCEPTOR_MODEL_RIGHT_MARGIN+ACCEPTOR_MODEL_LEFT_MARGIN) == false) { in Maxent_acceptor_prob_revcomp() 99515 if (sequence_okay(sequence,ACCEPTOR_MODEL_LEFT_MARGIN+ACCEPTOR_MODEL_RIGHT_MARGIN) == false) { in Maxent_acceptor_logodds() 99530 odds = score_acceptor_dinucleotide(sequence[ACCEPTOR_MODEL_LEFT_MARGIN-2], in Maxent_acceptor_logodds() 99531 sequence[ACCEPTOR_MODEL_LEFT_MARGIN-1])*maxentscore; in Maxent_acceptor_logodds()
|
H A D | chimera.c | 847 for (i = 0; i < ACCEPTOR_MODEL_LEFT_MARGIN - DONOR_MODEL_LEFT_MARGIN; i++) { in find_exonexon_fwd() 853 …acceptor_length = breakpoint_end - breakpoint_start + ACCEPTOR_MODEL_LEFT_MARGIN + ACCEPTOR_MODEL_… in find_exonexon_fwd() 870 for (i = 0; i < DONOR_MODEL_LEFT_MARGIN - ACCEPTOR_MODEL_LEFT_MARGIN; i++) { in find_exonexon_fwd() 878 for (i = DONOR_MODEL_LEFT_MARGIN, j = ACCEPTOR_MODEL_LEFT_MARGIN; in find_exonexon_fwd() 900 acceptor_prob_1 = Maxent_acceptor_prob(&(acceptor_ptr[j-ACCEPTOR_MODEL_LEFT_MARGIN])); in find_exonexon_fwd() 902 acceptor_altprob_1 = Maxent_acceptor_prob(&(acceptor_altptr[j-ACCEPTOR_MODEL_LEFT_MARGIN])); in find_exonexon_fwd() 984 for (i = 0; i < ACCEPTOR_MODEL_LEFT_MARGIN - DONOR_MODEL_LEFT_MARGIN; i++) { in find_exonexon_rev() 1007 for (i = 0; i < DONOR_MODEL_LEFT_MARGIN - ACCEPTOR_MODEL_LEFT_MARGIN; i++) { in find_exonexon_rev() 1015 for (i = DONOR_MODEL_LEFT_MARGIN, j = ACCEPTOR_MODEL_LEFT_MARGIN; in find_exonexon_rev() 1038 acceptor_prob_1 = Maxent_acceptor_prob(&(acceptor_ptr[j-ACCEPTOR_MODEL_LEFT_MARGIN])); in find_exonexon_rev() [all …]
|
H A D | maxent.h | 7 #define ACCEPTOR_MODEL_LEFT_MARGIN 20 /* Amount in intron. Includes AG */ macro
|
H A D | maxent_hr.c | 14 #define ACCEPTOR_MODEL_LEFT_MARGIN 20 /* Amount in intron. Includes AG */ macro 27305 if (splice_pos < chroffset + ACCEPTOR_MODEL_LEFT_MARGIN) { in Maxent_hr_acceptor_prob() 27308 startpos = splice_pos - ACCEPTOR_MODEL_LEFT_MARGIN; in Maxent_hr_acceptor_prob()
|
H A D | distant-rna.c | 479 if (segment_left + splice_pos_qend >= ACCEPTOR_MODEL_LEFT_MARGIN) { in find_spliceends_rna_plus() 997 if (segment_left + splice_pos_qend >= ACCEPTOR_MODEL_LEFT_MARGIN) { in find_spliceends_rna_minus()
|
H A D | pair.c | 2148 left = genomicpos - ACCEPTOR_MODEL_LEFT_MARGIN; in acceptor_score() 2149 …Genome_fill_buffer(&chrnum,&nunknowns,genome,left,ACCEPTOR_MODEL_LEFT_MARGIN+ACCEPTOR_MODEL_RIGHT_… in acceptor_score() 2153 printf("%*s^^\n",ACCEPTOR_MODEL_LEFT_MARGIN-2,""); in acceptor_score() 2164 …Genome_fill_buffer(&chrnum,&nunknowns,genome,left,ACCEPTOR_MODEL_LEFT_MARGIN+ACCEPTOR_MODEL_RIGHT_… in acceptor_score() 2165 make_complement_inplace(gbuffer,ACCEPTOR_MODEL_LEFT_MARGIN+ACCEPTOR_MODEL_RIGHT_MARGIN+1); in acceptor_score() 2169 printf("%*s^^\n",ACCEPTOR_MODEL_LEFT_MARGIN-2,""); in acceptor_score()
|
H A D | splice.c | 293 if (novelsplicingp && segmentj_left + splice_qpos_start >= ACCEPTOR_MODEL_LEFT_MARGIN) { in Splice_resolve_sense() 1204 if (novelsplicingp && segmentj_left + splice_qpos_start >= ACCEPTOR_MODEL_LEFT_MARGIN) { in Splice_resolve_antisense()
|
H A D | stage3.c | 12451 ACCEPTOR_MODEL_LEFT_MARGIN+ACCEPTOR_MODEL_RIGHT_MARGIN+1); in score_introns()
|