bool SeqTreeAsnizer::convertToTreeOption(const CRef< CAlgorithm_type >& alg, TreeOptions& treeOption)
{
//treeOption.alignUsage = CCd::USE_NORMAL_ALIGNMENT;
treeOption.cTermExt = alg->GetCTerminalExt();
treeOption.nTermExt = alg->GetNTerminalExt();
treeOption.clusteringMethod = (ETreeMethod)(alg->GetClustering_Method());
// bug fix. dih. eScoring_Scheme_aligned_score -> eScoring_Scheme_aligned_score_ext
treeOption.distMethod = (EDistMethod)((alg->GetScoring_Scheme() > CAlgorithm_type::eScoring_Scheme_aligned_score_ext) ?
alg->GetScoring_Scheme() - 1 : alg->GetScoring_Scheme());
treeOption.scope = (CAlgorithm_type::ETree_scope)((alg->IsSetTree_scope()) ?
alg->GetTree_scope() : CAlgorithm_type::eTree_scope_allDescendants);
treeOption.coloringScope = (CAlgorithm_type::EColoring_scope)((alg->IsSetColoring_scope()) ?
alg->GetColoring_scope() : CAlgorithm_type::eColoring_scope_allDescendants);
treeOption.matrix = (EScoreMatrixType)(
(alg->IsSetScore_Matrix()) ? alg->GetScore_Matrix(): CAlgorithm_type::eScore_Matrix_blosum62);
return true;
}
