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InspectOutfile Class Reference
[File IO]

#include <OpenMS/FORMAT/InspectOutfile.h>

List of all members.


Detailed Description

Representation of an Inspect outfile.

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
InspectOutfileoperator= (const InspectOutfile &inspect_outfile)
 assignment operator
bool operator== (const InspectOutfile &inspect_outfile) const
 equality operator
std::vector< UIntload (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< UIntgetWantedRecords (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< UIntgetSequences (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


Constructor & Destructor Documentation

InspectOutfile (  ) 

default constructor

InspectOutfile ( const InspectOutfile inspect_outfile  ) 

copy constructor

virtual ~InspectOutfile (  )  [virtual]

destructor


Member Function Documentation

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 
)

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


Member Data Documentation

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


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1