OpenMS  2.8.0
Public Member Functions | Private Member Functions | Private Attributes | List of all members
PepNovoInfile Class Reference

PepNovo input file adapter. More...

#include <OpenMS/FORMAT/PepNovoInfile.h>

Collaboration diagram for PepNovoInfile:

Public Member Functions

 PepNovoInfile ()
 default constructor More...
 PepNovoInfile (const PepNovoInfile &pepnovo_infile)
 copy constructor More...
virtual ~PepNovoInfile ()
 destructor More...
PepNovoInfileoperator= (const PepNovoInfile &pepnovo_infile)
 assignment operator More...
bool operator== (const PepNovoInfile &pepnovo_infile) const
 equality operator More...
void store (const String &filename)
void setModifications (const StringList &fixed_mods, const StringList &variable_mods)
 generates the PepNovo Infile for given fixed and variable modifications * More...
void getModifications (std::map< String, String > &modification_key_map) const
 return the modifications. More...

Private Member Functions

String handlePTMs_ (const String &modification, const bool variable)

Private Attributes

ModificationDefinitionsSet mods_
std::map< String, Stringmods_and_keys_
TextFile ptm_file_

Detailed Description

PepNovo input file adapter.

Creates a PepNovo_PTMs.txt file for PepNovo search.

Constructor & Destructor Documentation

◆ PepNovoInfile() [1/2]

default constructor

◆ PepNovoInfile() [2/2]

PepNovoInfile ( const PepNovoInfile pepnovo_infile)

copy constructor

◆ ~PepNovoInfile()

virtual ~PepNovoInfile ( )


Member Function Documentation

◆ getModifications()

void getModifications ( std::map< String, String > &  modification_key_map) const

return the modifications.

the modification unique identifiers are mapped to the keys used in the PepNovo Infile (origin+rounded monoisotopic mass of modification ). (e.g. modification_key_map["K+16"]=="Oxidation (K)" )

◆ handlePTMs_()

String handlePTMs_ ( const String modification,
const bool  variable 

retrieves the name of modification, and generates the corresponding line for the PepNovo infile.

modificationthe modification
variableshould be set to true if it variable

◆ operator=()

PepNovoInfile& operator= ( const PepNovoInfile pepnovo_infile)

assignment operator

◆ operator==()

bool operator== ( const PepNovoInfile pepnovo_infile) const

equality operator

◆ setModifications()

void setModifications ( const StringList fixed_mods,
const StringList variable_mods 

generates the PepNovo Infile for given fixed and variable modifications *

fixed_modsStringList of fixed modifications unique identifiers
variable_modsStringList of variable modifications unique identifiers

◆ store()

void store ( const String filename)

stores the experiment data in a PepNovo input file that can be used as input for PepNovo shell execution

filenamethe file which the input file is stored into
Exception::UnableToCreateFileis thrown if the given file could not be created

Member Data Documentation

◆ mods_

◆ mods_and_keys_

std::map<String, String> mods_and_keys_

◆ ptm_file_

TextFile ptm_file_