OpenMS  3.0.0
PepNovoInfile.h
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34 
35 #pragma once
36 
39 #include <OpenMS/FORMAT/TextFile.h>
40 
41 #include <map>
42 
43 
44 namespace OpenMS
45 {
53  class OPENMS_DLLAPI PepNovoInfile
54  {
55 public:
57  PepNovoInfile();
58 
60  PepNovoInfile(const PepNovoInfile & pepnovo_infile);
61 
63  virtual ~PepNovoInfile();
64 
66  PepNovoInfile & operator=(const PepNovoInfile & pepnovo_infile);
67 
69  bool operator==(const PepNovoInfile & pepnovo_infile) const;
70 
76  void store(const String & filename);
77 
83  void setModifications(const StringList & fixed_mods, const StringList & variable_mods);
84 
91  void getModifications(std::map<String, String> & modification_key_map) const;
92 
93 private:
95  std::map<String, String> mods_and_keys_;
97 
98 
104  String handlePTMs_(const String & modification, const bool variable);
105  };
106 
107 } // namespace OpenMS
108 
FileHandler.h
FileTypes.h
TextFile.h
OpenMS::PepNovoInfile::getModifications
void getModifications(std::map< String, String > &modification_key_map) const
return the modifications.
Size
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
ContactPerson.h
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
OpenMS::MascotGenericFile::store
void store(const String &filename, const PeakMap &experiment, bool compact=false)
stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell executio...
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
Int
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
SearchEngineBase.h
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
IdXMLFile.h
OpenMS::PepNovoOutfile
Representation of a PepNovo output file.
Definition: PepNovoOutfile.h:56
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::ProteinIdentification::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s, bool raw=false)
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::PepNovoInfile::ptm_file_
TextFile ptm_file_
Definition: PepNovoInfile.h:96
OpenMS::PepNovoOutfile::IndexPosMappingType
std::map< Size, std::pair< double, double > > IndexPosMappingType
Definition: PepNovoOutfile.h:60
QProcess
ModificationDefinitionsSet.h
MzXMLFile.h
DTAFile.h
OpenMS::PepNovoOutfile::load
void load(const std::string &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const double &score_threshold, const IndexPosMappingType &id_rt_mz, const std::map< String, String > &mod_id_map)
loads data from a PepNovo outfile
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
PepNovoInfile.h
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
MascotGenericFile.h
OpenMS::MascotGenericFile
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:62
OpenMS::PepNovoInfile::setModifications
void setModifications(const StringList &fixed_mods, const StringList &variable_mods)
generates the PepNovo Infile for given fixed and variable modifications *
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
PTMXMLFile.h
OpenMS::SearchEngineBase
Base class for Search Engine Adapters.
Definition: SearchEngineBase.h:54
ModificationsDB.h
IDMapper.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::PepNovoInfile::mods_
ModificationDefinitionsSet mods_
Definition: PepNovoInfile.h:94
OpenMS::PepNovoInfile::mods_and_keys_
std::map< String, String > mods_and_keys_
Definition: PepNovoInfile.h:95
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::PepNovoInfile::store
void store(const String &filename)
String.h
OpenMS::ModificationsDB::getAllSearchModifications
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
OpenMS::File::getTempDirectory
static String getTempDirectory()
OpenMS::PepNovoInfile
PepNovo input file adapter.
Definition: PepNovoInfile.h:53
OpenMS::File::removeDirRecursively
static bool removeDirRecursively(const String &dir_name)
Removes the subdirectories of the specified directory (absolute path). Returns true if successful.
PepNovoOutfile.h
File.h
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68