#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 |