| OpenMS 2.5.0

Public Member Functions | Static Protected Attributes | List of all members
InspectOutfile Class Reference
Format » File IO

Representation of an Inspect outfile. More...

`#include <OpenMS/FORMAT/InspectOutfile.h>`

## Public Member Functions

| InspectOutfile ()
| default constructor More...
| InspectOutfile (const InspectOutfile &inspect_outfile)
| copy constructor More...
virtual | ~InspectOutfile ()
| destructor More...
InspectOutfile & | operator= (const InspectOutfile &inspect_outfile)
| assignment operator More...
bool | operator== (const InspectOutfile &inspect_outfile) const
| equality operator More...
std::vector< Size > | load (const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const double p_value_threshold, const String &database_filename="")
std::vector< Size > | getWantedRecords (const String &result_filename, double p_value_threshold)
void | compressTrieDB (const String &database_filename, const String &index_filename, std::vector< Size > &wanted_records, const String &snd_database_filename, const String &snd_index_filename, bool append=false)
void | generateTrieDB (const String &source_database_filename, const String &database_filename, const String &index_filename, bool append=false, const String species="")
void | getACAndACType (String line, String &accession, String &accession_type)
void | getPrecursorRTandMZ (const std::vector< std::pair< String, std::vector< std::pair< Size, Size > > > > &files_and_peptide_identification_with_scan_number, std::vector< PeptideIdentification > &ids)
void | getLabels (const String &source_database_filename, String &ac_label, String &sequence_start_label, String &sequence_end_label, String &comment_label, String &species_label)
std::vector< Size > | getSequences (const String &database_filename, const std::map< Size, Size > &wanted_records, std::vector< String > &sequences)
void | getExperiment (PeakMap &exp, String &type, const String &in_filename)
bool | getSearchEngineAndVersion (const String &cmd_output, ProteinIdentification &protein_identification)
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, Size &number_of_columns)

## Static Protected Attributes

static const Size | db_pos_length_
| length of 1) More...
static const Size | trie_db_pos_length_
| length of 2) More...
static const Size | protein_name_length_
| length of 3) More...
static const Size | record_length_
| length of the whole record More...
static const char | trie_delimiter_
| the sequences in the trie database are delimited by this character More...
static const String | score_type_
| type of score More...

## Detailed Description

Representation of an Inspect outfile.

This class serves to read in an Inspect outfile and write an idXML file

Todo:
  Handle Modifications (Andreas)

## Constructor & Destructor Documentation

## ◆ InspectOutfile() [1/2]

InspectOutfile | ( |  | ) |

default constructor

## ◆ InspectOutfile() [2/2]

InspectOutfile | ( | const InspectOutfile & | inspect_outfile | ) |

copy constructor

## ◆ ~InspectOutfile()

virtual ~InspectOutfile | ( |  | ) |

virtual

destructor

## Member Function Documentation

## ◆ compressTrieDB()

void compressTrieDB | ( | const String & | database_filename,
|  | const String & | index_filename,
|  | std::vector< Size > & | wanted_records,
|  | const String & | snd_database_filename,
|  | const String & | snd_index_filename,
|  | bool | append = `false`
| ) |  |

generates a trie database from another one, using the wanted records only

Exceptions

  Exception::FileNotFound |
  Exception::ParseError |
  Exception::UnableToCreateFile |

## ◆ generateTrieDB()

void generateTrieDB | ( | const String & | source_database_filename,
|  | const String & | database_filename,
|  | const String & | index_filename,
|  | bool | append = `false`,
|  | const String | species = `""`
| ) |  |

generates a trie database from a given one (the type of database is determined by getLabels)

Exceptions

  Exception::FileNotFound |
  Exception::UnableToCreateFile |

## ◆ 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)

## ◆ getExperiment()

void getExperiment | ( | PeakMap & | exp,
|  | String & | type,
|  | const String & | in_filename
| ) |  |

inline

get the experiment from a file

Exceptions

  Exception::ParseError | is thrown if the file could not be parsed or the filetype could not be determined

References FileHandler::getTypeByContent(), FileHandler::loadExperiment(), ProgressLogger::NONE, MSExperiment::reset(), FileTypes::typeToName(), and FileTypes::UNKNOWN.

## ◆ getLabels()

void getLabels | ( | const String & | source_database_filename,
|  | String & | ac_label,
|  | String & | sequence_start_label,
|  | String & | sequence_end_label,
|  | String & | comment_label,
|  | String & | species_label
| ) |  |

retrieve the labels of a given database (at the moment FASTA and Swissprot)

Exceptions

  Exception::FileNotFound |
  Exception::ParseError |

## ◆ getPrecursorRTandMZ()

void getPrecursorRTandMZ | ( | const std::vector< std::pair< String, std::vector< std::pair< Size, Size > > > > & | files_and_peptide_identification_with_scan_number,
|  | std::vector< PeptideIdentification > & | ids
| ) |  |

retrieve the precursor retention time and mz value

Exceptions

  Exception::ParseError |

## ◆ getSearchEngineAndVersion()

bool getSearchEngineAndVersion | ( | const String & | cmd_output,
|  | ProteinIdentification & | protein_identification
| ) |  |

get the search engine and its version from the output of the InsPecT executable without parameters

returns true on success, false otherwise

## ◆ getSequences()

std::vector<Size> getSequences | ( | const String & | database_filename,
|  | const std::map< Size, Size > & | wanted_records,
|  | std::vector< String > & | sequences
| ) |  |

retrieve sequences from a trie database

Exceptions

  Exception::FileNotFound |

## ◆ getWantedRecords()

std::vector<Size> getWantedRecords | ( | const String & | result_filename,
|  | double | p_value_threshold
| ) |  |

loads only results which exceeds a given P-value threshold

Parameters

  result_filename | The filename of the results file
  p_value_threshold | Only identifications exceeding this threshold are read

Exceptions

  FileNotFound | is thrown is the file is not found
  FileEmpty | is thrown if the given file is empty

## ◆ load()

std::vector<Size> load | ( | const String & | result_filename,
|  | std::vector< PeptideIdentification > & | peptide_identifications,
|  | ProteinIdentification & | protein_identification,
|  | const double | p_value_threshold,
|  | const String & | database_filename = `""`
| ) |  |

load the results of an Inspect search

Parameters

  result_filename | Input parameter which is the file name of the input file
  peptide_identifications | Output parameter which holds the peptide identifications from the given file
  protein_identification | Output parameter which holds the protein identifications from the given file
  p_value_threshold |
  database_filename |

Exceptions

  FileNotFound | is thrown if the given file could not be found
  ParseError | is thrown if the given file could not be parsed
  FileEmpty | is thrown if the given file is empty

## ◆ operator=()

InspectOutfile& operator= | ( | const InspectOutfile & | inspect_outfile | ) |

assignment operator

## ◆ operator==()

bool operator== | ( | const InspectOutfile & | inspect_outfile | ) | const

equality operator

## ◆ readOutHeader()

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,
|  | Size & | number_of_columns
| ) |  |

read the header of an inspect output file and retrieve various information

Exceptions

  Exception::ParseError |

## Member Data Documentation

## ◆ db_pos_length_

const Size 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 protein's position in the trie database 3) the name of the protein (the line with the accession identifier)

## ◆ protein_name_length_

const Size protein_name_length_

static protected

length of 3)

## ◆ record_length_

const Size record_length_

static protected

length of the whole record

## ◆ score_type_

const String score_type_

static protected

type of score

## ◆ trie_db_pos_length_

const Size trie_db_pos_length_

static protected

length of 2)

## ◆ trie_delimiter_

const char trie_delimiter_

static protected

the sequences in the trie database are delimited by this character