RNPxl.C File Reference

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/FILTERING/TRANSFORMERS/Normalizer.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <QtCore/QStringList>
#include <QtCore/QProcess>
#include <QtCore/QObject>
#include <QFileInfo>
#include <algorithm>
#include <numeric>
#include <iostream>
#include <iomanip>
#include <fstream>

Classes
struct	RNPxlReportRow
struct	MarkerIonExtractor
struct	RNPxlReportRowHeader
struct	ModificationMassesResult
class	TOPPRNPxl
Defines
#define	RT_FACTOR   10000000
	Tool for RNP cross linking experiment analysis.
#define	RT_FACTOR_PRECISION   1000
#define	RT_MODULO_FACTOR   10000
#define	SEP   '\t'
Functions
bool	notInSeq (String res_seq, String query)
void	generateTargetSequences (const String &res_seq, Size pos, const map< char, vector< char > > &map_source2target, StringList &target_sequences)
ModificationMassesResult	initModificationMassesRNA (StringList target_nucleotides, StringList mappings, StringList restrictions, StringList modifications, String sequence_restriction, bool cysteine_adduct, Int max_length=4)
int	main (int argc, const char **argv)

---

Define Documentation

#define RT_FACTOR   10000000

Tool for RNP cross linking experiment analysis.

Referenced by TOPPRNPxl::main_().

#define RT_FACTOR_PRECISION   1000

Referenced by TOPPRNPxl::main_().

#define RT_MODULO_FACTOR   10000

#define SEP   '\t'

---

Function Documentation

void generateTargetSequences	(	const String &	res_seq,
		Size	pos,
		const map< char, vector< char > > &	map_source2target,
		StringList &	target_sequences
	)

Referenced by initModificationMassesRNA().

ModificationMassesResult initModificationMassesRNA	(	StringList	target_nucleotides,
		StringList	mappings,
		StringList	restrictions,
		StringList	modifications,
		String	sequence_restriction,
		bool	cysteine_adduct,
		Int	max_length = 4
	)

References OpenMS::Constants::c, generateTargetSequences(), EmpiricalFormula::getMonoWeight(), EmpiricalFormula::getString(), ModificationMassesResult::mod_combinations, ModificationMassesResult::mod_formula_idx, ModificationMassesResult::mod_masses, notInSeq(), String::prefix(), EmpiricalFormula::setCharge(), String::split(), and String::substitute().

Referenced by TOPPRNPxl::main_().

int main	(	int	argc,
		const char **	argv
	)

References TOPPBase::main().

bool notInSeq	(	String	res_seq,
		String	query
	)

References String::substr().

Referenced by initModificationMassesRNA().