Classes | |
struct | AdaptedIdentity |
struct | EquivalenceClassAA_ |
struct | FoundProteinFunctor |
struct | PAM30MS |
struct | SAValue< Index< StringSet< Peptide >, IndexWotd<> > > |
struct | ScoringMatrixData_< int, AminoAcid, AdaptedIdentity > |
struct | ScoringMatrixData_< int, AminoAcid, PAM30MS > |
Functions | |
template<bool enumerateA, bool enumerateB, typename TOnFoundFunctor , typename TTreeIteratorA , typename TIterPosA , typename TTreeIteratorB , typename TIterPosB , typename TErrors > | |
void | _approximateAminoAcidTreeSearch (TOnFoundFunctor &onFoundFunctor, TTreeIteratorA iterA, TIterPosA iterPosA, TTreeIteratorB iterB_, TIterPosB iterPosB, TErrors errorsLeft, TErrors classErrorsLeft) |
template<typename TEquivalenceTable > | |
bool | _charComparator (AminoAcid charA, AminoAcid charB, TEquivalenceTable equivalence) |
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inline |
References _charComparator().
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inline |
References FoundProteinFunctor::addHit(), FoundProteinFunctor::filter_passed, FoundProteinFunctor::filter_rejected, File::findDatabase(), StopWatch::getClockTime(), StopWatch::getCPUTime(), EnzymaticDigestion::getEnzymeByName(), EnzymaticDigestion::getSpecificityByName(), Map< Key, T >::has(), String::hasPrefix(), String::hasSuffix(), IdXMLFile::load(), FASTAFile::load(), LOG_ERROR, LOG_INFO, LOG_WARN, main(), EnzymaticDigestion::NamesOfEnzymes, EnzymaticDigestion::NamesOfSpecificity, FoundProteinFunctor::pep_to_prot, File::readable(), String::remove(), PeptideEvidence::setAAAfter(), PeptideEvidence::setAABefore(), ProteinHit::setAccession(), PeptideEvidence::setEnd(), EnzymaticDigestion::setEnzyme(), PeptideEvidence::setProteinAccession(), ProteinHit::setSequence(), EnzymaticDigestion::setSpecificity(), PeptideEvidence::setStart(), EnzymaticDigestion::SIZE_OF_ENZYMES, EnzymaticDigestion::SIZE_OF_SPECIFICITY, StopWatch::start(), StopWatch::stop(), IdXMLFile::store(), and String::substitute().
Referenced by _approximateAminoAcidTreeSearch().
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |