C++ (Cpp) prepare_ComplexSequenceEvalSet Examples

Example #1

File: genestats.c Project: PlantandFoodResearch/wise2

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;
}

Example #2

File: complexevalset.c Project: PlantandFoodResearch/wise2

ComplexSequenceEvalSet * default_dna_ComplexSequenceEvalSet(void)
{
  ComplexSequenceEvalSet * out;

  out = ComplexSequenceEvalSet_alloc_len(1);

  add_ComplexSequenceEvalSet(out,base_number_ComplexSequenceEval());

  out->type = SEQUENCE_DNA;

  prepare_ComplexSequenceEvalSet(out);

  return out;
}

Example #3

File: complexevalset.c Project: PlantandFoodResearch/wise2

ComplexSequenceEvalSet * default_aminoacid_ComplexSequenceEvalSet(void)
{
  ComplexSequenceEvalSet * out;


  out = ComplexSequenceEvalSet_alloc_len(1);

  add_ComplexSequenceEvalSet(out,aminoacid_number_ComplexSequenceEval());

  out->type = SEQUENCE_PROTEIN;

  prepare_ComplexSequenceEvalSet(out);

  return out;
}

Example #4

File: complexevalset.c Project: PlantandFoodResearch/wise2

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;
}

Example #5

File: genestats.c Project: mrmckain/RefTrans

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;
}