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SequestOutfile Class Reference
[File IO]

#include <OpenMS/FORMAT/SequestOutfile.h>

List of all members.


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.

Public Member Functions

 SequestOutfile ()
 Constructor.
 SequestOutfile (const SequestOutfile &sequest_outfile)
 copy constructor
virtual ~SequestOutfile ()
 destructor
SequestOutfileoperator= (const SequestOutfile &sequest_outfile)
 assignment operator
bool operator== (const SequestOutfile &sequest_outfile) const
 equality operator
void load (const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const Real p_value_threshold, std::vector< Real > &pvalues, const String &database="") throw (Exception::FileNotFound, Exception::ParseError, Exception::IllegalArgument)
 loads data from a Sequest outfile
bool getColumns (const String &line, std::vector< String > &substrings, UInt number_of_columns, UInt reference_column)
 retrieve columns from a Sequest outfile line
void getSequences (const String &database_filename, const std::map< String, UInt > &ac_position_map, std::vector< String > &sequences, std::vector< std::pair< String, UInt > > &found, std::map< String, UInt > &not_found) throw (Exception::FileNotFound)
 retrieve sequences from a FASTA database
void getACAndACType (String line, String &accession, String &accession_type)
void readOutHeader (const String &result_filename, DateTime &datetime, Real &precursor_mz_value, Int &charge, UInt &precursor_mass_type, UInt &ion_mass_type, UInt &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, UInt &number_of_columns) throw (Exception::FileNotFound, Exception::ParseError)
 read the header of an out file and retrieve various informations

Static Private Attributes

static Real const_weights_ []
static Real xcorr_weights_ []
static Real delta_cn_weights_ []
static Real rank_sp_weights_ []
static Real delta_mass_weights_ []
static UInt max_pep_lens_ []
static UInt num_frags_ []


Constructor & Destructor Documentation

SequestOutfile (  ) 

Constructor.

SequestOutfile ( const SequestOutfile sequest_outfile  ) 

copy constructor

virtual ~SequestOutfile (  )  [virtual]

destructor


Member Function Documentation

SequestOutfile& operator= ( const SequestOutfile sequest_outfile  ) 

assignment operator

bool operator== ( const SequestOutfile sequest_outfile  )  const

equality operator

void load ( const String result_filename,
std::vector< PeptideIdentification > &  peptide_identifications,
ProteinIdentification protein_identification,
const Real  p_value_threshold,
std::vector< Real > &  pvalues,
const String database = "" 
) throw (Exception::FileNotFound, Exception::ParseError, Exception::IllegalArgument)

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

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

retrieve columns from a Sequest outfile line

void getSequences ( const String database_filename,
const std::map< String, UInt > &  ac_position_map,
std::vector< String > &  sequences,
std::vector< std::pair< String, UInt > > &  found,
std::map< String, UInt > &  not_found 
) throw (Exception::FileNotFound)

retrieve sequences from a FASTA database

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)

void readOutHeader ( const String result_filename,
DateTime datetime,
Real precursor_mz_value,
Int charge,
UInt precursor_mass_type,
UInt ion_mass_type,
UInt 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,
UInt number_of_columns 
) throw (Exception::FileNotFound, Exception::ParseError)

read the header of an out file and retrieve various informations


Member Data Documentation

Real const_weights_[] [static, private]

Real xcorr_weights_[] [static, private]

Real delta_cn_weights_[] [static, private]

Real rank_sp_weights_[] [static, private]

Real delta_mass_weights_[] [static, private]

UInt max_pep_lens_[] [static, private]

UInt num_frags_[] [static, private]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:45 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1