ScoreModels scoreModels = ScoreModels.getInstance();
for (ScoreModelI sm : scoreModels.getModels())
{
- if (!forPasimap && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
+ if ((!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
|| sm.isSecondaryStructure() && ssPresent))
{