Functions | |
| void | getBYSeries (AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, UInt charge=1u) |
| Helper functions for the DIA scoring of OpenSWATH. More... | |
| void | getTheorMasses (AASequence &a, std::vector< double > &masses, UInt charge=1u) |
| for SWATH – get the theoretical b and y series masses for a sequence More... | |
| void | getAveragineIsotopeDistribution (double product_mz, std::vector< std::pair< double, double > > &isotopesSpec, double charge=1., int nr_isotopes=4, double mannmass=1.00048) |
| get averagine distribution given mass More... | |
| void | simulateSpectrumFromAASequence (AASequence &aa, std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.) |
| simulate spectrum from AASequence More... | |
| void | modifyMassesByCharge (const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, double charge=1.) |
| modify masses by charge More... | |
| void | addPreisotopeWeights (const std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeSpec, UInt nrpeaks=2, double preIsotopePeaksWeight=-0.5, double mannmass=1.000482, double charge=1.) |
| add negative preisotope weights to spectrum More... | |
| void | addIsotopes2Spec (const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.) |
| given an experimental spectrum add isotope pattern. More... | |
| void | sortByFirst (std::vector< std::pair< double, double > > &tmp) |
| sorts vector of pairs by first More... | |
| void | extractFirst (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass) |
| extract first from vector of pairs More... | |
| void | extractSecond (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass) |
| extract second from vector of pairs More... | |
| void OpenMS::DIAHelpers::addIsotopes2Spec | ( | const std::vector< std::pair< double, double > > & | spec, |
| std::vector< std::pair< double, double > > & | isotopeMasses, | ||
| double | charge = 1. |
||
| ) |
given an experimental spectrum add isotope pattern.
| void OpenMS::DIAHelpers::addPreisotopeWeights | ( | const std::vector< double > & | firstIsotopeMasses, |
| std::vector< std::pair< double, double > > & | isotopeSpec, | ||
| UInt | nrpeaks = 2, |
||
| double | preIsotopePeaksWeight = -0.5, |
||
| double | mannmass = 1.000482, |
||
| double | charge = 1. |
||
| ) |
add negative preisotope weights to spectrum
| void OpenMS::DIAHelpers::extractFirst | ( | const std::vector< std::pair< double, double > > & | peaks, |
| std::vector< double > & | mass | ||
| ) |
extract first from vector of pairs
| void OpenMS::DIAHelpers::extractSecond | ( | const std::vector< std::pair< double, double > > & | peaks, |
| std::vector< double > & | mass | ||
| ) |
extract second from vector of pairs
| void OpenMS::DIAHelpers::getAveragineIsotopeDistribution | ( | double | product_mz, |
| std::vector< std::pair< double, double > > & | isotopesSpec, | ||
| double | charge = 1., |
||
| int | nr_isotopes = 4, |
||
| double | mannmass = 1.00048 |
||
| ) |
get averagine distribution given mass
| void OpenMS::DIAHelpers::getBYSeries | ( | AASequence & | a, |
| std::vector< double > & | bseries, | ||
| std::vector< double > & | yseries, | ||
| UInt | charge = 1u |
||
| ) |
Helper functions for the DIA scoring of OpenSWATH.
compute the b and y series masses for a given AASequence
| void OpenMS::DIAHelpers::getTheorMasses | ( | AASequence & | a, |
| std::vector< double > & | masses, | ||
| UInt | charge = 1u |
||
| ) |
for SWATH – get the theoretical b and y series masses for a sequence
| void OpenMS::DIAHelpers::modifyMassesByCharge | ( | const std::vector< std::pair< double, double > > & | masses, |
| std::vector< std::pair< double, double > > & | modmass, | ||
| double | charge = 1. |
||
| ) |
modify masses by charge
| [in] | modmass | [out] |
| void OpenMS::DIAHelpers::simulateSpectrumFromAASequence | ( | AASequence & | aa, |
| std::vector< double > & | firstIsotopeMasses, | ||
| std::vector< std::pair< double, double > > & | isotopeMasses, | ||
| double | charge = 1. |
||
| ) |
simulate spectrum from AASequence
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:37 using doxygen 1.8.5 |