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Searched refs:ACCEPTOR_MODEL_LEFT_MARGIN (Results 1 – 8 of 8) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dmaxent.c99341 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 Dchimera.c847 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()
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H A Dmaxent.h7 #define ACCEPTOR_MODEL_LEFT_MARGIN 20 /* Amount in intron. Includes AG */ macro
H A Dmaxent_hr.c14 #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 Ddistant-rna.c479 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 Dpair.c2148 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 Dsplice.c293 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 Dstage3.c12451 ACCEPTOR_MODEL_LEFT_MARGIN+ACCEPTOR_MODEL_RIGHT_MARGIN+1); in score_introns()