| OpenMS 2.5.0

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

Representation of a Sequest output file. More...

`#include <OpenMS/FORMAT/SequestOutfile.h>`

## Public Member Functions

| SequestOutfile ()
| Constructor. More...
| SequestOutfile (const SequestOutfile &sequest_outfile)
| copy constructor More...
virtual | ~SequestOutfile ()
| destructor More...
SequestOutfile & | operator= (const SequestOutfile &sequest_outfile)
| assignment operator More...
bool | operator== (const SequestOutfile &sequest_outfile) const
| equality operator More...
void | load (const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const double p_value_threshold, std::vector< double > &pvalues, const String &database="", const bool ignore_proteins_per_peptide=false)
| loads data from a Sequest outfile More...
bool | getColumns (const String &line, std::vector< String > &substrings, Size number_of_columns, Size reference_column)
| retrieve columns from a Sequest outfile line More...
void | getSequences (const String &database_filename, const std::map< String, Size > &ac_position_map, std::vector< String > &sequences, std::vector< std::pair< String, Size > > &found, std::map< String, Size > &not_found)
void | getACAndACType (String line, String &accession, String &accession_type)
void | readOutHeader (const String &result_filename, DateTime &datetime, double &precursor_mz_value, Int &charge, Size &precursor_mass_type, Size &ion_mass_type, Size &displayed_peptides, String &sequest, String &sequest_version, String &database_type, Int &number_column, Int &rank_sp_column, Int &id_column, Int &mh_column, Int &delta_cn_column, Int &xcorr_column, Int &sp_column, Int &sf_column, Int &ions_column, Int &reference_column, Int &peptide_column, Int &score_column, Size &number_of_columns)

## Static Private Attributes

static double | const_weights_ []
static double | xcorr_weights_ []
static double | delta_cn_weights_ []
static double | rank_sp_weights_ []
static double | delta_mass_weights_ []
static Size | max_pep_lens_ []
static Size | num_frags_ []

## Detailed Description

Representation of a Sequest output file.

This class serves to read in a Sequest outfile. The information can be retrieved via the load function.

Todo:

  Handle Modifications (Andreas)

  Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas)

## Constructor & Destructor Documentation

## ◆ SequestOutfile() [1/2]

SequestOutfile | ( |  | ) |

Constructor.

## ◆ SequestOutfile() [2/2]

SequestOutfile | ( | const SequestOutfile & | sequest_outfile | ) |

copy constructor

## ◆ ~SequestOutfile()

virtual ~SequestOutfile | ( |  | ) |

virtual

destructor

## Member Function Documentation

## ◆ getACAndACType()

void getACAndACType | ( | String | line,
|  | String & | accession,
|  | String & | accession_type
| ) |  |

retrieve the accession type and accession number from a protein description line (e.g. from FASTA line: >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus], get ac:AAD44166.1 ac type: GenBank)

## ◆ getColumns()

bool getColumns | ( | const String & | line,
|  | std::vector< String > & | substrings,
|  | Size | number_of_columns,
|  | Size | reference_column
| ) |  |

retrieve columns from a Sequest outfile line

## ◆ getSequences()

void getSequences | ( | const String & | database_filename,
|  | const std::map< String, Size > & | ac_position_map,
|  | std::vector< String > & | sequences,
|  | std::vector< std::pair< String, Size > > & | found,
|  | std::map< String, Size > & | not_found
| ) |  |

retrieve sequences from a FASTA database

Parameters

  database_filename |
  ac_position_map |
  sequences |
  found |
  not_found |

Exceptions

  Exception::FileNotFound | is thrown if the database file could not be found

## ◆ load()

void load | ( | const String & | result_filename,
|  | std::vector< PeptideIdentification > & | peptide_identifications,
|  | ProteinIdentification & | protein_identification,
|  | const double | p_value_threshold,
|  | std::vector< double > & | pvalues,
|  | const String & | database = `""`,
|  | const bool | ignore_proteins_per_peptide = `false`
| ) |  |

loads data from a Sequest outfile

Parameters

  result_filename | the file to be loaded
  peptide_identifications | the identifications
  protein_identification | the protein identifications
  p_value_threshold | the significance level (for the peptide hit scores)
  pvalues | a list with the pvalues of the peptides (pvalues computed with peptide prophet)
  database | the database used for the search
  ignore_proteins_per_peptide | this is a hack to deal with files that use a suffix like "+1" in column "Reference", but do not actually list extra protein references in subsequent lines

Exceptions

  Exception::FileNotFound | is thrown if the given result file could not be found
  Exception::ParseError | is thrown if the given result file could not be parsed
  Exception::IllegalArgument | This class serves to read in a Sequest outfile. The information can be retrieved via the load function.

## ◆ operator=()

SequestOutfile& operator= | ( | const SequestOutfile & | sequest_outfile | ) |

assignment operator

## ◆ operator==()

bool operator== | ( | const SequestOutfile & | sequest_outfile | ) | const

equality operator

## ◆ readOutHeader()

void readOutHeader | ( | const String & | result_filename,
|  | DateTime & | datetime,
|  | double & | precursor_mz_value,
|  | Int & | charge,
|  | Size & | precursor_mass_type,
|  | Size & | ion_mass_type,
|  | Size & | displayed_peptides,
|  | String & | sequest,
|  | String & | sequest_version,
|  | String & | database_type,
|  | Int & | number_column,
|  | Int & | rank_sp_column,
|  | Int & | id_column,
|  | Int & | mh_column,
|  | Int & | delta_cn_column,
|  | Int & | xcorr_column,
|  | Int & | sp_column,
|  | Int & | sf_column,
|  | Int & | ions_column,
|  | Int & | reference_column,
|  | Int & | peptide_column,
|  | Int & | score_column,
|  | Size & | number_of_columns
| ) |  |

read the header of an out file and retrieve various information

Exceptions

  Exception::FileNotFound | is thrown if the results file could not be found
  Exception::ParseError | is thrown if the results file could not be parsed

## Member Data Documentation

## ◆ const_weights_

double const_weights_[]

static private

## ◆ delta_cn_weights_

double delta_cn_weights_[]

static private

## ◆ delta_mass_weights_

double delta_mass_weights_[]

static private

## ◆ max_pep_lens_

Size max_pep_lens_[]

static private

## ◆ num_frags_

Size num_frags_[]

static private

## ◆ rank_sp_weights_

double rank_sp_weights_[]

static private

## ◆ xcorr_weights_

double xcorr_weights_[]

static private