PepNovoInfile Class Reference

PepNovo input file adapter. More...

#include <OpenMS/FORMAT/PepNovoInfile.h>

Public Member Functions
	PepNovoInfile ()
	default constructor More...
	PepNovoInfile (const PepNovoInfile &pepnovo_infile)
	copy constructor More...
virtual	~PepNovoInfile ()
	destructor More...
PepNovoInfile &	operator= (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, String >	mods_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]

PepNovoInfile

(

)

default constructor

PepNovoInfile() [2/2]

PepNovoInfile

(

const PepNovoInfile &

pepnovo_infile

)

copy constructor

~PepNovoInfile()

virtual ~PepNovoInfile ( )

virtual

destructor

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  )

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

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 *

Parameters

fixed_mods	StringList of fixed modifications unique identifiers
variable_mods	StringList 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

Parameters

filename

the file which the input file is stored into

Exceptions

Exception::UnableToCreateFile

is thrown if the given file could not be created

Member Data Documentation

mods_

ModificationDefinitionsSet mods_

private

mods_and_keys_

std::map<String, String> mods_and_keys_

private

ptm_file_

TextFile ptm_file_

private