ComplexSequenceEval * ComplexSequenceEval_from_pwmDNAScore_splice(SpliceSiteScore * score)
{
ComplexSequenceEval * out;
/* printf("Making CSE from %d\n",score);*/
out = ComplexSequenceEval_alloc();
/* shouldn't really add ones, but this is ok anyway.
Yukky hack due to not understanding a bug in the window
determination
*/
/**
*STILL don't know precisely what is going on down here! ***/
/* out->left_window = ssm->offset + ssm->pre_splice_site +1; */
out->left_window =10;
/* out->right_window = ssm->offset + ssm->post_splice_site +1; */
out->right_window =10;
out->left_lookback =10;
out->outside_score= NEGI;
out->data_type = 245; /* any old key */
out->data = (void *) score;
out->type = SEQUENCE_GENOMIC;
out->eval_func = pwmDNA_splice_ComplexSequence_eval_func;
out->score_type = CseScoreType_Bits;
return out;
}
ComplexSequenceEval * flat_negi(void)
{
ComplexSequenceEval * out;
out= ComplexSequenceEval_alloc();
out->left_window = 0;
out->right_window = 0;
out->outside_score = NEGI;
out->eval_func = flat_negi_eval;
return out;
}
ComplexSequenceEval * stupid_3SS(void)
{
ComplexSequenceEval * out;
out= ComplexSequenceEval_alloc();
out->left_window = 3;
out->right_window = 3;
out->left_lookback = 5;
out->outside_score = NEGI;
out->eval_func = stupid_3SS_eval;
return out;
}
ComplexSequenceEval * aminoacid_number_ComplexSequenceEval(void)
{
ComplexSequenceEval * out;
out = ComplexSequenceEval_alloc();
if (out == NULL ) {
return NULL;
}
out->left_window = out->right_window = 0;
out->eval_func = aminoacid_number_func;
return out;
}
ComplexSequenceEval * ComplexSequenceEval_for_scored_gt(Score * score_for_gt)
{
ComplexSequenceEval * out;
out = ComplexSequenceEval_alloc();
out->left_window = 3;
out->right_window = 7;
out->left_lookback = 8;
out->outside_score = NEGI;
out->data = (void*) score_for_gt;
out->type = SEQUENCE_GENOMIC;
out->eval_func = scored_gt_eval_func;
out->score_type = CseScoreType_Bits;
return out;
}
ComplexSequenceEval * codon64_number_ComplexSequenceEval(void)
{
ComplexSequenceEval * out;
out = ComplexSequenceEval_alloc();
if (out == NULL ) {
return NULL;
}
out->left_window = 2;
out->right_window = 0;
out->outside_score = 65;
out->eval_func = codon64_number_func;
return out;
}
ComplexSequenceEval * ComplexSequenceEval_from_SpliceSiteModel(SpliceSiteModel * ssm)
{
ComplexSequenceEval * out;
out = ComplexSequenceEval_alloc();
/* shouldn't really add ones, but this is ok anyway.
Yukky hack due to not understanding a bug in the window
determination
*/
/* out->left_window = ssm->offset + ssm->pre_splice_site +1; */
out->left_window = 11;
/* out->right_window = ssm->offset + ssm->post_splice_site +1; */
out->right_window = 8;
out->outside_score= NEGI;
out->data_type = SPLICESITEMODELER_TYPE;
out->data = ssm;
out->type = SEQUENCE_GENOMIC;
out->eval_func = SpliceSiteModeler_ComplexSequence_eval_func;
return out;
}
