#include <OpenMS/FORMAT/SequestOutfile.h>
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 | |
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 | |
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 > ¬_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_ [] |
SequestOutfile | ( | ) |
Constructor.
SequestOutfile | ( | const SequestOutfile & | sequest_outfile | ) |
copy constructor
virtual ~SequestOutfile | ( | ) | [virtual] |
destructor
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
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 |
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
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
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] |
Generated Tue Apr 1 15:36:45 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |