#include <OpenMS/FORMAT/InspectOutfile.h>
This class serves to read in an Inspect outfile and write an IdXML file
Public Member Functions | |
InspectOutfile () | |
default constructor | |
InspectOutfile (const InspectOutfile &inspect_outfile) | |
copy constructor | |
virtual | ~InspectOutfile () |
destructor | |
InspectOutfile & | operator= (const InspectOutfile &inspect_outfile) |
assignment operator | |
bool | operator== (const InspectOutfile &inspect_outfile) const |
equality operator | |
std::vector< UInt > | load (const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const Real p_value_threshold, const String &database_filename="") throw (Exception::FileNotFound, Exception::ParseError, Exception::IllegalArgument, Exception::FileEmpty) |
load the results of an Inspect search | |
std::vector< UInt > | getWantedRecords (const String &result_filename, Real p_value_threshold) throw (Exception::FileNotFound, Exception::FileEmpty, Exception::IllegalArgument) |
void | compressTrieDB (const String &database_filename, const String &index_filename, std::vector< UInt > &wanted_records, const String &snd_database_filename, const String &snd_index_filename, bool append=false) throw (Exception::FileNotFound, Exception::ParseError, Exception::UnableToCreateFile) |
generates a trie database from another one, using the wanted records only | |
void | generateTrieDB (const String &source_database_filename, const String &database_filename, const String &index_filename, bool append=false, const String species="") throw (Exception::FileNotFound, Exception::UnableToCreateFile) |
generates a trie database from a given one (the type of database is determined by getLabels) | |
void | getACAndACType (String line, String &accession, String &accession_type) |
void | getPrecursorRTandMZ (const std::vector< std::pair< String, std::vector< std::pair< UInt, UInt > > > > &files_and_peptide_identification_with_scan_number, std::vector< PeptideIdentification > &ids) throw (Exception::ParseError) |
retvrieve the precursor retention time and mz value | |
void | getLabels (const String &source_database_filename, String &ac_label, String &sequence_start_label, String &sequence_end_label, String &comment_label, String &species_label) throw (Exception::FileNotFound, Exception::ParseError) |
retrieve the labes of a given database (at the moment FASTA and Swissprot) | |
std::vector< UInt > | getSequences (const String &database_filename, const std::map< UInt, UInt > &wanted_records, std::vector< String > &sequences) throw (Exception::FileNotFound) |
retrieve sequences from a trie database | |
template<typename PeakT> | |
void | getExperiment (MSExperiment< PeakT > &exp, String &type, const String &in_filename) throw (Exception::ParseError) |
get the experiment from a file | |
void | getSearchEngineAndVersion (const String &inspect_output_without_parameters_filename, ProteinIdentification &protein_identification) throw (Exception::FileNotFound) |
get the search engine and its version from a file with the output of InsPecT without parameters | |
void | readOutHeader (const String &filename, const String &header_line, Int &spectrum_file_column, Int &scan_column, Int &peptide_column, Int &protein_column, Int &charge_column, Int &MQ_score_column, Int &p_value_column, Int &record_number_column, Int &DB_file_pos_column, Int &spec_file_pos_column, UInt &number_of_columns) throw (Exception::ParseError) |
read the header of an inspect output file and retrieve various informations | |
Static Protected Attributes | |
static const UInt | db_pos_length_ |
length of 1) | |
static const UInt | trie_db_pos_length_ |
length of 2) | |
static const UInt | protein_name_length_ |
length of 3) | |
static const UInt | record_length_ |
length of the whole record | |
static const char | trie_delimiter_ |
the sequences in the trie database are delimited by this character | |
static const String | score_type_ |
type of score |
InspectOutfile | ( | ) |
default constructor
InspectOutfile | ( | const InspectOutfile & | inspect_outfile | ) |
copy constructor
virtual ~InspectOutfile | ( | ) | [virtual] |
destructor
InspectOutfile& operator= | ( | const InspectOutfile & | inspect_outfile | ) |
assignment operator
bool operator== | ( | const InspectOutfile & | inspect_outfile | ) | const |
equality operator
std::vector< UInt > load | ( | const String & | result_filename, | |
std::vector< PeptideIdentification > & | peptide_identifications, | |||
ProteinIdentification & | protein_identification, | |||
const Real | p_value_threshold, | |||
const String & | database_filename = "" | |||
) | throw (Exception::FileNotFound, Exception::ParseError, Exception::IllegalArgument, Exception::FileEmpty) |
load the results of an Inspect search
std::vector< UInt > getWantedRecords | ( | const String & | result_filename, | |
Real | p_value_threshold | |||
) | throw (Exception::FileNotFound, Exception::FileEmpty, Exception::IllegalArgument) |
void compressTrieDB | ( | const String & | database_filename, | |
const String & | index_filename, | |||
std::vector< UInt > & | wanted_records, | |||
const String & | snd_database_filename, | |||
const String & | snd_index_filename, | |||
bool | append = false | |||
) | throw (Exception::FileNotFound, Exception::ParseError, Exception::UnableToCreateFile) |
generates a trie database from another one, using the wanted records only
void generateTrieDB | ( | const String & | source_database_filename, | |
const String & | database_filename, | |||
const String & | index_filename, | |||
bool | append = false , |
|||
const String | species = "" | |||
) | throw (Exception::FileNotFound, Exception::UnableToCreateFile) |
generates a trie database from a given one (the type of database is determined by getLabels)
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 getPrecursorRTandMZ | ( | const std::vector< std::pair< String, std::vector< std::pair< UInt, UInt > > > > & | files_and_peptide_identification_with_scan_number, | |
std::vector< PeptideIdentification > & | ids | |||
) | throw (Exception::ParseError) |
retvrieve the precursor retention time and mz value
void getLabels | ( | const String & | source_database_filename, | |
String & | ac_label, | |||
String & | sequence_start_label, | |||
String & | sequence_end_label, | |||
String & | comment_label, | |||
String & | species_label | |||
) | throw (Exception::FileNotFound, Exception::ParseError) |
retrieve the labes of a given database (at the moment FASTA and Swissprot)
std::vector< UInt > getSequences | ( | const String & | database_filename, | |
const std::map< UInt, UInt > & | wanted_records, | |||
std::vector< String > & | sequences | |||
) | throw (Exception::FileNotFound) |
retrieve sequences from a trie database
void getExperiment | ( | MSExperiment< PeakT > & | exp, | |
String & | type, | |||
const String & | in_filename | |||
) | throw (Exception::ParseError) [inline] |
get the experiment from a file
void getSearchEngineAndVersion | ( | const String & | inspect_output_without_parameters_filename, | |
ProteinIdentification & | protein_identification | |||
) | throw (Exception::FileNotFound) |
get the search engine and its version from a file with the output of InsPecT without parameters
void readOutHeader | ( | const String & | filename, | |
const String & | header_line, | |||
Int & | spectrum_file_column, | |||
Int & | scan_column, | |||
Int & | peptide_column, | |||
Int & | protein_column, | |||
Int & | charge_column, | |||
Int & | MQ_score_column, | |||
Int & | p_value_column, | |||
Int & | record_number_column, | |||
Int & | DB_file_pos_column, | |||
Int & | spec_file_pos_column, | |||
UInt & | number_of_columns | |||
) | throw (Exception::ParseError) |
read the header of an inspect output file and retrieve various informations
const UInt db_pos_length_ [static, protected] |
length of 1)
a record in the index file that belongs to a trie database consists of three parts 1) the protein's position in the original database 2) the proteins's position in the trie database 3) the name of the protein (the line with the accession identifier)
const UInt trie_db_pos_length_ [static, protected] |
length of 2)
const UInt protein_name_length_ [static, protected] |
length of 3)
const UInt record_length_ [static, protected] |
length of the whole record
const char trie_delimiter_ [static, protected] |
the sequences in the trie database are delimited by this character
const String score_type_ [static, protected] |
type of score
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |