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 DoubleReal p_value_threshold, std::vector< DoubleReal > &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 > ¬_found) |
| void | getACAndACType (String line, String &accession, String &accession_type) |
| void | readOutHeader (const String &result_filename, DateTime &datetime, DoubleReal &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 DoubleReal | const_weights_ [] |
| static DoubleReal | xcorr_weights_ [] |
| static DoubleReal | delta_cn_weights_ [] |
| static DoubleReal | rank_sp_weights_ [] |
| static DoubleReal | delta_mass_weights_ [] |
| static Size | max_pep_lens_ [] |
| static Size | num_frags_ [] |
Representation of a Sequest output file.
This class serves to read in a Sequest outfile. The information can be retrieved via the load function.
Handle Modifications (Andreas)
Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas)
| SequestOutfile | ( | ) |
Constructor.
| SequestOutfile | ( | const SequestOutfile & | sequest_outfile | ) |
copy constructor
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virtual |
destructor
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)
| bool getColumns | ( | const String & | line, |
| std::vector< String > & | substrings, | ||
| Size | number_of_columns, | ||
| Size | reference_column | ||
| ) |
retrieve columns from a Sequest outfile line
| 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
| database_filename | |
| ac_position_map | |
| sequences | |
| found | |
| not_found |
| Exception::FileNotFound | is thrown if the database filen could not be found |
| void load | ( | const String & | result_filename, |
| std::vector< PeptideIdentification > & | peptide_identifications, | ||
| ProteinIdentification & | protein_identification, | ||
| const DoubleReal | p_value_threshold, | ||
| std::vector< DoubleReal > & | pvalues, | ||
| const String & | database = "", |
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| const bool | ignore_proteins_per_peptide = false |
||
| ) |
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 |
| 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 |
| 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. |
| SequestOutfile& operator= | ( | const SequestOutfile & | sequest_outfile | ) |
assignment operator
| bool operator== | ( | const SequestOutfile & | sequest_outfile | ) | const |
equality operator
| void readOutHeader | ( | const String & | result_filename, |
| DateTime & | datetime, | ||
| DoubleReal & | 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
| Exception::FileNotFound | is thrown if the results file could not be found |
| Exception::ParseError | is thrown if the results file could not be parsed |
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |