| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | List of all members
MRMFeaturePickerFile Class Reference

_MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file. More...

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

Inheritance diagram for MRMFeaturePickerFile:

## Public Member Functions

| MRMFeaturePickerFile ()=default
| Constructor. More...
| ~MRMFeaturePickerFile ()=default
| Destructor. More...
void | load (const String &filename, std::vector< MRMFeaturePicker::ComponentParams > &cp_list, std::vector< MRMFeaturePicker::ComponentGroupParams > &cgp_list)
| Loads the file's data and saves it into vectors of `ComponentParams` and `ComponentGroupParams`. More...
Public Member Functions inherited from CsvFile
| CsvFile ()
| Default constructor. More...
| ~CsvFile () override
| destructor More...
| CsvFile (const String &filename, char is=',', bool ie=false, Int first_n=-1)
| Constructor with filename. More...
void | load (const String &filename, char is=',', bool ie=false, Int first_n=-1)
| Loads data from a text file. More...
void | store (const String &filename)
| Stores the buffer's content into a file. More...
void | addRow (const StringList &list)
| Add a row to the buffer. More...
void | clear ()
| Clears the buffer. More...
bool | getRow (Size row, StringList &list)
| writes all items from a row to list More...
std::vector< String >::size_type | rowCount () const
| Returns the number of rows that were loaded from the file. More...

## Protected Member Functions

bool | extractParamsFromLine_ (const StringList &line, const std::map< String, Size > &headers, MRMFeaturePicker::ComponentParams &cp, MRMFeaturePicker::ComponentGroupParams &cgp) const
| Extracts the information from a `StringList` and saves it into the correct data structures. More...
void | setCastValue_ (const String &key, const String &value, Param &params) const
| Helper method which takes care of converting the given value to the desired type, based on the header (here `key`) information. More...

## Detailed Description

_MRMFeaturePickerFile_ loads components and components groups parameters from a .csv file.

The structures defined in [MRMFeaturePicker](MRMFeaturePicker) are used.

It is required that columns `component_name` and `component_group_name` are present. Lines whose `component_name`'s or `component_group_name`'s value is an empty string, will be skipped. The class supports the absence of information within other columns.

A reduced example of the expected format (fewer columns are shown here): > component_name,component_group_name,TransitionGroupPicker:stop_after_feature,TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length > arg-L.arg-L_1.Heavy,arg-L,2,15 > arg-L.arg-L_1.Light,arg-L,2,17 > orn.orn_1.Heavy,orn,3,21 > orn.orn_1.Light,orn,3,13

## Constructor & Destructor Documentation

## ◆ MRMFeaturePickerFile()

MRMFeaturePickerFile | ( |  | ) |

default

Constructor.

## ◆ ~MRMFeaturePickerFile()

~MRMFeaturePickerFile | ( |  | ) |

default

Destructor.

## Member Function Documentation

## ◆ extractParamsFromLine_()

bool extractParamsFromLine_ | ( | const StringList & | line,
|  | const std::map< String, Size > & | headers,
|  | MRMFeaturePicker::ComponentParams & | cp,
|  | MRMFeaturePicker::ComponentGroupParams & | cgp
| ) |  | const

protected

Extracts the information from a `StringList` and saves it into the correct data structures.

Parameters

  [in] | line | The line parsed from the input file
  [in] | headers | A mapping from a given header to its value's position
  [out] | cp | The extracted component parameters
  [out] | cgp | The extracted component group parameters

Returns
  Returns `false` if `component_name` or `component_group_name` are empty strings. Otherwise, it returns `true`.

## ◆ load()

void load | ( | const String & | filename,
|  | std::vector< MRMFeaturePicker::ComponentParams > & | cp_list,
|  | std::vector< MRMFeaturePicker::ComponentGroupParams > & | cgp_list
| ) |  |

Loads the file's data and saves it into vectors of `ComponentParams` and `ComponentGroupParams`.

The file is expected to contain at least two columns: `component_name` and `component_group_name`. Otherwise, an exception is thrown.

If a component group (identified by its name) is found multiple times, only the first one is saved.

Parameters

  [in] | filename | Path to the .csv input file
  [out] | cp_list | Component params are saved in this list
  [out] | cgp_list | Component Group params are saved in this list

Exceptions

  Exception::MissingInformation | If the required columns are not found.
  Exception::FileNotFound | If input file is not found.

## ◆ setCastValue_()

void setCastValue_ | ( | const String & | key,
|  | const String & | value,
|  | Param & | params
| ) |  | const

protected

Helper method which takes care of converting the given value to the desired type, based on the header (here `key`) information.

Parameters

  [in] | key | The header name with which the correct conversion is chosen
  [in] | value | The value to be converted
  [in,out] | params | The object where the new value is saved