#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 |
Macros | |
#define | RT_FACTOR 10000000 |
#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 RT_FACTOR 10000000 |
Referenced by TOPPRNPxl::main_().
#define RT_FACTOR_PRECISION 1000 |
Referenced by TOPPRNPxl::main_().
#define RT_MODULO_FACTOR 10000 |
Referenced by TOPPRNPxl::main_().
#define SEP '\t' |
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().
References String::substr().
Referenced by initModificationMassesRNA().
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:23 using doxygen 1.8.5 |