NuXLAnnotateAndLocate.cpp File Reference

#include "NuXLFragmentIonGenerator.h"
#include "NuXLAnnotateAndLocate.h"
#include <OpenMS/CHEMISTRY/IonNaming.h>
#include "NuXLFragmentAnnotationHelper.h"
#include "NuXLConstants.h"
#include <OpenMS/ANALYSIS/XLMS/OPXLSpectrumProcessingAlgorithms.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/Macros.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <regex>

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

Typedefs
using	MapIonIndexToFragmentAnnotation = map< Size, vector< NuXLFragmentAnnotationHelper::FragmentAnnotationDetail_ > >

Functions
static PeakSpectrum	createTotalLossSpectrumForAnnotations (const AASequence &fixed_and_variable_modified_peptide, size_t precursor_charge, Param new_param)
static void	removeDuplicatedPeaks (MSSpectrum &spec)
	Removes duplicate peaks based on their m/z values.
static vector< PeptideHit::PeakAnnotation >	createIonCentricFragmentAnnotationsForUnshiftedIons (const PeakSpectrum &total_loss_spectrum, const PeakSpectrum &exp_spectrum, const vector< pair< Size, Size > > &alignment, set< Size > &peak_is_annotated, vector< PeptideHit::PeakAnnotation > &annotated_precursor_ions, MapIonIndexToFragmentAnnotation &unshifted_b_ions, MapIonIndexToFragmentAnnotation &unshifted_y_ions, MapIonIndexToFragmentAnnotation &unshifted_a_ions, vector< PeptideHit::PeakAnnotation > &unshifted_loss_ions, vector< PeptideHit::PeakAnnotation > &annotated_immonium_ions)