Scoring of an spectrum given library intensities of a transition group. More...
#include <OpenMS/ANALYSIS/OPENSWATH/DIAPrescoring.h>
Public Member Functions | |
| DiaPrescore () | |
| DiaPrescore (double dia_extract_window, int nr_isotopes=4, int nr_charges=4) | |
| void | defineDefaults () |
| void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. | |
| void | score (OpenSwath::SpectrumPtr spec, const std::vector< OpenSwath::LightTransition > <, double &dotprod, double &manhattan) |
| Score a spectrum given a transition group. | |
| void | operator() (OpenSwath::SpectrumAccessPtr swath_ptr, OpenSwath::LightTargetedExperiment &transition_exp_used, OpenSwath::IDataFrameWriter *ivw) |
| Compute manhattan and dotprod score for all spectra which can be accessed by the SpectrumAccessPtr for all transitions groups in the LightTargetedExperiment. | |
Private Attributes | |
| double | dia_extract_window_ |
| int | nr_isotopes_ |
| int | nr_charges_ |
Detailed Description
Scoring of an spectrum given library intensities of a transition group.
In DIA (data independent acquisition) / SWATH analysis, at each chromatographic point a full MS2 spectrum is recorded. This class allows to compute a number of scores based on the full MS2 spectrum available. The scores are the following:
See also class DIAScoring.
Simulate theoretical spectrum from library intensities of transition group and compute manhattan distance and dotprod score between spectrum intentensities and simulated spectrum.
Constructor & Destructor Documentation
| DiaPrescore | ( | ) |
| DiaPrescore | ( | double | dia_extract_window, | |
| int | nr_isotopes = 4, |
|||
| int | nr_charges = 4 | |||
| ) |
Member Function Documentation
| void defineDefaults | ( | ) |
| void operator() | ( | OpenSwath::SpectrumAccessPtr | swath_ptr, | |
| OpenSwath::LightTargetedExperiment & | transition_exp_used, | |||
| OpenSwath::IDataFrameWriter * | ivw | |||
| ) |
Compute manhattan and dotprod score for all spectra which can be accessed by the SpectrumAccessPtr for all transitions groups in the LightTargetedExperiment.
| void score | ( | OpenSwath::SpectrumPtr | spec, | |
| const std::vector< OpenSwath::LightTransition > & | lt, | |||
| double & | dotprod, | |||
| double & | manhattan | |||
| ) |
Score a spectrum given a transition group.
Simulate theoretical spectrum from library intensities of transition group and compute manhattan distance and dotprod score between spectrum intentensities and simulated spectrum.
| void updateMembers_ | ( | ) | [virtual] |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
Member Data Documentation
double dia_extract_window_ [private] |
int nr_charges_ [private] |
int nr_isotopes_ [private] |
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |