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PepNovoInfile Class Reference
[File IO]

#include <OpenMS/FORMAT/PepNovoInfile.h>

List of all members.


Detailed Description

PepNovo input file adapter.

Creates a pepnovo.params file for PepNovo search from a peak list.

Public Member Functions

 PepNovoInfile ()
 default constructor
 PepNovoInfile (const PepNovoInfile &pepnovo_infile)
 copy constructor
virtual ~PepNovoInfile ()
 destructor
PepNovoInfileoperator= (const PepNovoInfile &pepnovo_infile)
 assignment operator
bool operator== (const PepNovoInfile &pepnovo_infile) const
 equality operator
String store (const String &filename) throw (Exception::UnableToCreateFile)
 stores the experiment data in a PepNovo input file that can be used as input for PepNovo shell execution
void handlePTMs (const String &modification_line, const String &modifications_filename, const bool monoisotopic) throw (Exception::FileNotReadable, Exception::FileNotFound, Exception::ParseError)
 retrieves the name, mass change, affected residues, type and position for all modifications from a string
const std::map< String,
std::vector< String > > & 
getModifications () const
 return the modifications (the modification names map to the affected residues, the mass change and the type)

Private Attributes

std::map< String, std::vector
< String > > 
PTMname_residues_mass_type_
 the modification names map to the affected residues, the mass change and the type


Constructor & Destructor Documentation

PepNovoInfile (  ) 

default constructor

PepNovoInfile ( const PepNovoInfile pepnovo_infile  ) 

copy constructor

virtual ~PepNovoInfile (  )  [virtual]

destructor


Member Function Documentation

PepNovoInfile& operator= ( const PepNovoInfile pepnovo_infile  ) 

assignment operator

bool operator== ( const PepNovoInfile pepnovo_infile  )  const

equality operator

String store ( const String filename  )  throw (Exception::UnableToCreateFile)

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

void handlePTMs ( const String modification_line,
const String modifications_filename,
const bool  monoisotopic 
) throw (Exception::FileNotReadable, Exception::FileNotFound, Exception::ParseError)

retrieves the name, mass change, affected residues, type and position for all modifications from a string

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

return the modifications (the modification names map to the affected residues, the mass change and the type)


Member Data Documentation

std::map< String, std::vector< String > > PTMname_residues_mass_type_ [private]

the modification names map to the affected residues, the mass change and the type


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1