ComplexSequenceEvalSet * new_ComplexSequenceEvalSet_from_GeneModel(GeneModel * gm) { ComplexSequenceEvalSet * out; assert(gm); assert(gm->splice5score); assert(gm->splice3score); out = ComplexSequenceEvalSet_alloc_len(11); add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval()); add_ComplexSequenceEvalSet(out,codon_number_ComplexSequenceEval()); if( gm->use_gtag_splice == FALSE ) { add_ComplexSequenceEvalSet(out,ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice5score)); add_ComplexSequenceEvalSet(out,ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice3score)); } else { add_ComplexSequenceEvalSet(out,ComplexSequenceEval_for_scored_gt(&gm->score_for_gtag)); add_ComplexSequenceEvalSet(out,ComplexSequenceEval_for_scored_ag(&gm->score_for_gtag)); } add_ComplexSequenceEvalSet(out,flat_zero()); add_ComplexSequenceEvalSet(out,flat_zero()); out->type = SEQUENCE_GENOMIC; prepare_ComplexSequenceEvalSet(out); return out; }
ComplexSequenceEvalSet * default_genomic_ComplexSequenceEvalSet(void) { ComplexSequenceEvalSet * out; out = ComplexSequenceEvalSet_alloc_len(11); add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval()); add_ComplexSequenceEvalSet(out,codon_number_ComplexSequenceEval()); add_ComplexSequenceEvalSet(out,stupid_5SS()); add_ComplexSequenceEvalSet(out,stupid_3SS()); add_ComplexSequenceEvalSet(out,flat_zero()); add_ComplexSequenceEvalSet(out,flat_zero()); out->type = SEQUENCE_GENOMIC; prepare_ComplexSequenceEvalSet(out); return out; }
ComplexSequenceEvalSet * new_ComplexSequenceEvalSet_from_GeneModel(GeneModel * gm) { ComplexSequenceEvalSet * out; assert(gm); assert(gm->splice5score); assert(gm->splice3score); out = ComplexSequenceEvalSet_alloc_len(11); add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval()); add_ComplexSequenceEvalSet(out,codon_number_ComplexSequenceEval()); add_ComplexSequenceEvalSet(out,ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice5score)); add_ComplexSequenceEvalSet(out,ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice3score)); add_ComplexSequenceEvalSet(out,flat_zero()); add_ComplexSequenceEvalSet(out,flat_zero()); out->type = SEQUENCE_GENOMIC; prepare_ComplexSequenceEvalSet(out); return out; }