| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
OpenSwathOSWWriter Class Reference

Class to write out an OpenSwath OSW SQLite output (PyProphet input). More...

`#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.h>`

## Public Member Functions

| OpenSwathOSWWriter (const String &output_filename, const String &input_filename="inputfile", bool ms1_scores=false, bool sonar=false, bool uis_scores=false)
bool | isActive () const
void | writeHeader ()
| Initializes file by generating SQLite tables. More...
String | getScore (const Feature &feature, std::string score_name) const
| Prepare scores for SQLite insertion. More...
std::vector< String > | getSeparateScore (const Feature &feature, std::string score_name) const
| Prepare concatenated scores for SQLite insertion. More...
String | prepareLine (const OpenSwath::LightCompound &, const OpenSwath::LightTransition *, FeatureMap &output, String id) const
| Prepare a single line (feature) for output. More...
void | writeLines (const std::vector< String > &to_osw_output)
| Write data to disk. More...

## Private Attributes

String | output_filename_
String | input_filename_
OpenMS::UInt64 | run_id_
bool | doWrite_
bool | use_ms1_traces_
bool | sonar_
bool | enable_uis_scoring_

## Detailed Description

Class to write out an OpenSwath OSW SQLite output (PyProphet input).

The class can take a FeatureMap and create a set of string from it suitable for output to OSW using the prepareLine function. The SQL data is directly linked to the PQP file format described in the TransitionPQPFile class. See also OpenSwathTSVWriter for another output format.

The file format has the following tables:

RUN
ID | INT | Primary Key (run id)
FILENAME | TEXT | Original filename associated with the run

FEATURE
ID | INT | Primary Key (feature id)
RUN_ID | INT | Foreign Key (RUN.ID)
PRECURSOR_ID | INT | Foreign Key (TransitionPQPFile PRECURSOR.ID)
EXP_RT | REAL | Experimental RT (retention time) of the feature
NORM_RT | REAL | Normalized RT (retention time) of the feature. The position of the peak group in the normalized retention time space (e.g. fx(RT) where fx describes the transformation fx)
DELTA_RT | REAL | The difference in retention between expected retention time of the assay and the measured feature retention time (EXP_RT)
LEFT_WIDTH | REAL | Retention time start of the peak (left width) in seconds
RIGHT_WIDTH | REAL | Retention time end of the peak (right width) in seconds

FEATURE_MS1
FEATURE_ID | INT | Foreign Key (FEATURE.ID)
AREA_INTENSITY | REAL | Precursor intensity (area)
APEX_INTENSITY | REAL | Precursor intensity (apex)
VAR_... | REAL | Precursor score used in pyProphet

FEATURE_MS2
FEATURE_ID | INT | Foreign Key (FEATURE.ID)
AREA_INTENSITY | REAL | Summed fragment ion intensity (area)
TOTAL_AREA_INTENSITY | REAL | Summed total XIC of the whole chromatogram
APEX_INTENSITY | REAL | Summed fragment ion intensity (apex)
TOTAL_MI | REAL | Total mutual information (MI)
VAR_... | REAL | Fragment ion score used in pyProphet

FEATURE_PRECURSOR
FEATURE_ID | INT | Foreign Key (FEATURE.ID)
ISOTOPE | INT | Isotope identifier
AREA_INTENSITY | REAL | Precursor isotope ion intensity (area)
APEX_INTENSITY | REAL | Precursor isotope ion intensity (apex)

FEATURE_TRANSITION
FEATURE_ID | INT | Foreign Key (FEATURE.ID)
TRANSITION_ID | INT | Foreign Key (transition identifier)
AREA_INTENSITY | REAL | Fragment ion intensity (area)
TOTAL_AREA_INTENSITY | REAL | Total XIC of the whole chromatogram
APEX_INTENSITY | REAL | Fragment ion intensity (apex)
TOTAL_MI | REAL | Total mutual information (MI)
VAR_... | REAL | Fragment ion score used in pyProphet

## Constructor & Destructor Documentation

## ◆ OpenSwathOSWWriter()

OpenSwathOSWWriter | ( | const String & | output_filename,
|  | const String & | input_filename = `"inputfile"`,
|  | bool | ms1_scores = `false`,
|  | bool | sonar = `false`,
|  | bool | uis_scores = `false`
| ) |  |

inline

## Member Function Documentation

## ◆ getScore()

String getScore | ( | const Feature & | feature,
|  | std::string | score_name
| ) |  | const

Prepare scores for SQLite insertion.

Some scores might not be defined, those are reported as NULL

Parameters

  feature | The feature being evaluated
  score_name | The name of the queried score

Returns
  A string with the queried score

## ◆ getSeparateScore()

std::vector<String> getSeparateScore | ( | const Feature & | feature,
|  | std::string | score_name
| ) |  | const

Prepare concatenated scores for SQLite insertion.

Some scores might not be defined, those are reported as NULL

Parameters

  feature | The feature being evaluated
  score_name | The name of the queried score

Returns
  A vector of strings with the queried scores

## ◆ isActive()

bool isActive | ( |  | ) | const

## ◆ prepareLine()

String prepareLine | ( | const OpenSwath::LightCompound & | ,
|  | const OpenSwath::LightTransition * | ,
|  | FeatureMap & | output,
|  | String | id
| ) |  | const

Prepare a single line (feature) for output.

The result can be flushed to disk using writeLines (either line by line or after collecting several lines).

Parameters

  pep | The compound (peptide/metabolite) used for extraction
  transition | The transition used for extraction
  output | The feature map containing all features (each feature will generate one entry in the output)
  id | The transition group identifier (peptide/metabolite id)

Returns
  A string to be written using writeLines

## ◆ writeHeader()

void writeHeader | ( |  | ) |

Initializes file by generating SQLite tables.

## ◆ writeLines()

void writeLines | ( | const std::vector< String > & | to_osw_output | ) |

Write data to disk.

Takes a set of pre-prepared data statements from prepareLine and flushes them to disk

Parameters

  to_osw_output | Statements generated by prepareLine

Note
  Try to call this function as little as possible (it opens a new database connection each time)
  Only call inside an OpenMP critical section

## Member Data Documentation

## ◆ doWrite_

bool doWrite_

private

## ◆ enable_uis_scoring_

bool enable_uis_scoring_

private

## ◆ input_filename_

String input_filename_

private

## ◆ output_filename_

String output_filename_

private

## ◆ run_id_

OpenMS::UInt64 run_id_

private

## ◆ sonar_

bool sonar_

private

## ◆ use_ms1_traces_

bool use_ms1_traces_

private