| OpenMS 2.5.0

Public Member Functions | Private Member Functions | Private Attributes | List of all members
PepNovoInfile Class Reference
Format » File IO

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