PepNovoInfile Class Reference [File IO]

PepNovo input file adapter. More...

#include <OpenMS/FORMAT/PepNovoInfile.h>

List of all members.

Public Member Functions
	PepNovoInfile ()
	default constructor
	PepNovoInfile (const PepNovoInfile &pepnovo_infile)
	copy constructor
virtual	~PepNovoInfile ()
	destructor
PepNovoInfile &	operator= (const PepNovoInfile &pepnovo_infile)
	assignment operator
bool	operator== (const PepNovoInfile &pepnovo_infile) const
	equality operator
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 *
void	getModifications (std::map< String, String > &modification_key_map) const
	return the modifications.
Private Member Functions
String	handlePTMs_ (const String &modification, const bool variable)
Private Attributes
ModificationDefinitionsSet	mods_
std::map< String, String >	mods_and_keys_
TextFile	ptm_file_

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Detailed Description

PepNovo input file adapter.

Creates a PepNovo_PTMs.txt file for PepNovo search.

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Constructor & Destructor Documentation

PepNovoInfile

(

)

default constructor

PepNovoInfile

(

const PepNovoInfile &

pepnovo_infile

)

copy constructor

virtual ~PepNovoInfile

(

)

[virtual]

destructor

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Member Function Documentation

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)" )

String handlePTMs_	(	const String &	modification,
		const bool	variable
	)			[private]

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

Parameters:

	modification	the modification
	variable	should be set to true if it variable

PepNovoInfile& operator=

(

const PepNovoInfile &

pepnovo_infile

)

assignment operator

bool operator==

(

const PepNovoInfile &

pepnovo_infile

)

const

equality operator

void setModifications	(	const StringList &	fixed_mods,
		const StringList &	variable_mods
	)

generates the PepNovo Infile for given fixed and variable modifications *

Parameters:

	fixed_mods	StringList of fixed modifications unique identifiers
	variable_mods	StringList of variable modifications unique identifiers

void store

(

const String &

filename

)

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

Parameters:

filename

the file which the input file is stored into

Exceptions:

Exception::UnableToCreateFile

is thrown if the given file could not be created

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Member Data Documentation

ModificationDefinitionsSet mods_ [private]

std::map<String, String> mods_and_keys_ [private]

TextFile ptm_file_ [private]