OpenMS
SequestOutfile Class Reference

Representation of a Sequest output file. More...

#include <OpenMS/FORMAT/SequestOutfile.h>

Collaboration diagram for SequestOutfile:
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Public Member Functions

 SequestOutfile ()
 Constructor. More...
 
 SequestOutfile (const SequestOutfile &sequest_outfile)
 copy constructor More...
 
virtual ~SequestOutfile ()
 destructor More...
 
SequestOutfileoperator= (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]

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::FileNotFoundis 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_filenamethe file to be loaded
peptide_identificationsthe identifications
protein_identificationthe protein identifications
p_value_thresholdthe significance level (for the peptide hit scores)
pvaluesa list with the pvalues of the peptides (pvalues computed with peptide prophet)
databasethe database used for the search
ignore_proteins_per_peptidethis 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::FileNotFoundis thrown if the given result file could not be found
Exception::ParseErroris thrown if the given result file could not be parsed
Exception::IllegalArgumentThis 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::FileNotFoundis thrown if the results file could not be found
Exception::ParseErroris thrown if the results file could not be parsed

Member Data Documentation

◆ const_weights_

double const_weights_[]
staticprivate

◆ delta_cn_weights_

double delta_cn_weights_[]
staticprivate

◆ delta_mass_weights_

double delta_mass_weights_[]
staticprivate

◆ max_pep_lens_

Size max_pep_lens_[]
staticprivate

◆ num_frags_

Size num_frags_[]
staticprivate

◆ rank_sp_weights_

double rank_sp_weights_[]
staticprivate

◆ xcorr_weights_

double xcorr_weights_[]
staticprivate