| OpenMS 2.5.0

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

Used to load and store xQuest result files. More...

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

Inheritance diagram for XQuestResultXMLFile:

## Public Member Functions

| XQuestResultXMLFile ()
| ~XQuestResultXMLFile () override
void | load (const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
| Load the content of the xquest.xml file into the provided data structures. More...
void | store (const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
| Stores the identifications in a xQuest XML file. More...
int | getNumberOfHits () const
| Returns the total number of hits in the file. More...
double | getMinScore () const
| Returns minimum score among the hits in the file. More...
double | getMaxScore () const
| Returns maximum score among the hits in the file. More...
Public Member Functions inherited from XMLFile
| XMLFile ()
| Default constructor. More...
| XMLFile (const String &schema_location, const String &version)
| Constructor that sets the schema location. More...
virtual | ~XMLFile ()
| Destructor. More...
bool | isValid (const String &filename, std::ostream &os)
| Checks if a file validates against the XML schema. More...
const String & | getVersion () const
| return the version of the schema More...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Static Public Member Functions

static void | writeXQuestXMLSpec (const String &out_file, const String &base_name, const OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, const std::vector< std::pair< Size, Size > > &spectrum_pairs, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra)
| Writes spec.xml output containing matching peaks between heavy and light spectra after comparing and filtering. More...
static void | writeXQuestXMLSpec (const String &out_file, const String &base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra)
| Writes spec.xml output containing spectra for visualization. This version of the function is meant to be used for label-free linkers. More...

## Static Private Member Functions

static String | getxQuestBase64EncodedSpectrum_ (const PeakSpectrum &spec, String header)
| Transforms a PeakSpectrum into a base 64 encoded string, which is the format used in spec.xml for xQuest. More...
static void | wrap_ (const String &input, Size width, String &output)
| A helper function, that takes one string containing one line and wraps it into several lines of a given width. More...

## Private Attributes

int | n_hits_
| Total number of hits within the result file. More...
double | min_score_
| Minimum score encountered in file. More...
double | max_score_
| Maximum score encountered in file. More...

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
Protected Member Functions inherited from XMLFile
void | parse_ (const String &filename, XMLHandler *handler)
| Parses the XML file given by `filename` using the handler given by `handler`. More...
void | parseBuffer_ (const std::string &buffer, XMLHandler *handler)
| Parses the in-memory buffer given by `buffer` using the handler given by `handler`. More...
void | save_ (const String &filename, XMLHandler *handler) const
| Stores the contents of the XML handler given by `handler` in the file given by `filename`. More...
void | enforceEncoding_ (const String &encoding)
Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. More...
Protected Attributes inherited from XMLFile
String | schema_location_
| XML schema file location. More...
String | schema_version_
| Version string. More...
String | enforced_encoding_
| Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

Used to load and store xQuest result files.

These files are used to store results derived from chemical cross-linking coupled to MS experiments.

A documented schema for this format can be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS

## Constructor & Destructor Documentation

## ◆ XQuestResultXMLFile()

XQuestResultXMLFile | ( |  | ) |

## ◆ ~XQuestResultXMLFile()

~XQuestResultXMLFile | ( |  | ) |

override

## Member Function Documentation

## ◆ getMaxScore()

double getMaxScore | ( |  | ) | const

Returns maximum score among the hits in the file.

Returns
  Maximum score among the hits in the file.

## ◆ getMinScore()

double getMinScore | ( |  | ) | const

Returns minimum score among the hits in the file.

Returns
  Minimum score among the hits in the file.

## ◆ getNumberOfHits()

int getNumberOfHits | ( |  | ) | const

Returns the total number of hits in the file.

Returns
  total number of hits in the file

## ◆ getxQuestBase64EncodedSpectrum_()

static String getxQuestBase64EncodedSpectrum_ | ( | const PeakSpectrum & | spec,
|  | String | header
| ) |  |

static private

Transforms a PeakSpectrum into a base 64 encoded string, which is the format used in spec.xml for xQuest.

Parameters

  The | spectrum
  A | header for the spectrum, build using the base_name parameter for writeXQuestXMLSpec and the index of the spectrum.

## ◆ load()

void load | ( | const String & | filename,
|  | std::vector< PeptideIdentification > & | pep_ids,
|  | std::vector< ProteinIdentification > & | prot_ids
| ) |  |

Load the content of the xquest.xml file into the provided data structures.

Parameters

  filename | Filename of the file which is to be loaded.
  pep_ids | Where the spectra with identifications of the input file will be loaded to.
  prot_ids | Where the protein identification of the input file will be loaded to.

## ◆ store()

void store | ( | const String & | filename,
|  | const std::vector< ProteinIdentification > & | poid,
|  | const std::vector< PeptideIdentification > & | peid
| ) |  | const

Stores the identifications in a xQuest XML file.

Exceptions

  Exception::UnableToCreateFile | is thrown if the file could not be created

## ◆ wrap_()

static void wrap_ | ( | const String & | input,
|  | Size | width,
|  | String & | output
| ) |  |

static private

A helper function, that takes one string containing one line and wraps it into several lines of a given width.

Parameters

  The | string as one line
  The | preferred line width
  String | in which the output is written

## ◆ writeXQuestXMLSpec() [1/2]

static void writeXQuestXMLSpec | ( | const String & | out_file,
|  | const String & | base_name,
|  | const OPXLDataStructs::PreprocessedPairSpectra & | preprocessed_pair_spectra,
|  | const std::vector< std::pair< Size, Size > > & | spectrum_pairs,
|  | const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > & | all_top_csms,
|  | const PeakMap & | spectra
| ) |  |

static

Writes spec.xml output containing matching peaks between heavy and light spectra after comparing and filtering.

Parameters

  Path | and filename for the output file
  The | base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra.
  The | preprocessed spectra after comparing and filtering
  Indices | of spectrum pairs in the input map
  CrossLinkSpectrumMatches,from | which the IDs were generated. Only spectra with matches are written out.
  The | spectra, that were searched as a PeakMap. The indices in spectrum_pairs correspond to spectra in this map.

## ◆ writeXQuestXMLSpec() [2/2]

static void writeXQuestXMLSpec | ( | const String & | out_file,
|  | const String & | base_name,
|  | const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > & | all_top_csms,
|  | const PeakMap & | spectra
| ) |  |

static

Writes spec.xml output containing spectra for visualization. This version of the function is meant to be used for label-free linkers.

Parameters

  Path | and filename for the output file
  The | base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra.
  CrossLinkSpectrumMatches,from | which the IDs were generated. Only spectra with matches are written out.
  The | spectra, that were searched as a PeakMap.

## Member Data Documentation

## ◆ max_score_

double max_score_

private

Maximum score encountered in file.

## ◆ min_score_

double min_score_

private

Minimum score encountered in file.

## ◆ n_hits_

int n_hits_

private

Total number of hits within the result file.