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| | DIAScoring () |
| | Default constructor. More...
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| virtual | ~DIAScoring () |
| | Destructor. More...
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| void | set_dia_parameters (double dia_extract_window, double dia_centroided, double dia_byseries_intensity_min, double dia_byseries_ppm_diff, double dia_nr_isotopes, double dia_nr_charges) |
| | set parameters for the algorithm More...
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| void | dia_isotope_scores (const std::vector< TransitionType > &transitions, SpectrumType spectrum, OpenSwath::IMRMFeature *mrmfeature, double &isotope_corr, double &isotope_overlap) |
| | Isotope scores, see class description. More...
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| void | dia_massdiff_score (const std::vector< TransitionType > &transitions, SpectrumType spectrum, const std::vector< double > &normalized_library_intensity, double &ppm_score, double &ppm_score_weighted) |
| | Massdiff scores, see class description. More...
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| void | dia_by_ion_score (SpectrumType spectrum, AASequence &sequence, int charge, double &bseries_score, double &yseries_score) |
| | b/y ion scores More...
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| void | score_with_isotopes (SpectrumType spectrum, const std::vector< TransitionType > &transitions, double &dotprod, double &manhattan) |
| | Dotproduct / Manhatten score with theoretical spectrum. More...
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Public Member Functions inherited from DefaultParamHandler |
| | DefaultParamHandler (const String &name) |
| | Constructor with name that is displayed in error messages. More...
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| | DefaultParamHandler (const DefaultParamHandler &rhs) |
| | Copy constructor. More...
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| virtual | ~DefaultParamHandler () |
| | Destructor. More...
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| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| | Assignment operator. More...
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| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| | Equality operator. More...
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| void | setParameters (const Param ¶m) |
| | Sets the parameters. More...
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| const Param & | getParameters () const |
| | Non-mutable access to the parameters. More...
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| const Param & | getDefaults () const |
| | Non-mutable access to the default parameters. More...
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| const String & | getName () const |
| | Non-mutable access to the name. More...
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| void | setName (const String &name) |
| | Mutable access to the name. More...
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| const std::vector< String > & | getSubsections () const |
| | Non-mutable access to the registered subsections. More...
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| | DIAScoring (const DIAScoring &rhs) |
| | Copy constructor (algorithm class) More...
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| DIAScoring & | operator= (const DIAScoring &rhs) |
| | Assignment operator (algorithm class) More...
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| void | updateMembers_ () |
| | Synchronize members with param class. More...
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| void | diaIsotopeScoresSub_ (const std::vector< TransitionType > &transitions, SpectrumType spectrum, std::map< std::string, double > &intensities, double &isotope_corr, double &isotope_overlap) |
| | Subfunction of dia_isotop_scores. More...
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| void | getFirstIsotopeRelativeIntensities_ (const std::vector< TransitionType > &transitions, OpenSwath::IMRMFeature *mrmfeature, std::map< std::string, double > &intensities) |
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| DoubleReal | largePeaksBeforeFirstIsotope_ (double product_mz, SpectrumType &spectrum, double max_ppm_diff, double main_peak) |
| | Search for a large peak _before_ (lower m/z) the current peak. More...
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| DoubleReal | scoreIsotopePattern_ (double product_mz, const std::vector< double > &isotopes_int, int putative_fragment_charge) |
| | Compare an experimental isotope pattern to a theoretical one. More...
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Scoring of an spectrum at the peak apex of an chromatographic elution peak.
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:
- isotope scores: – isotope_corr: computes the correlation of each fragment ion with the theoretical isotope distribution. – isotope_overlap: checks whether a signal at position (mz - 1) / charge exists and how strong it is. This would be an indication that the current peak is an isotopic signal of another peak.
- massdiff score: computes the difference in ppm of the experimental signal to the exepcted signal
- b/y ion score: checks for the presence of b/y ions of the peptide in question
- theoretical spectrum: a dotproduct and a manhattan score with a theoretical spectrum
This class expects spectra objects that implement the OpenSWATH Spectrum interface. Transitions are expected to be in the light transition format (defined in OPENSWATHALGO/DATAACCESS/TransitionExperiment.h).