| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | List of all members
MRMFeatureQCFile Class Reference
Format » File IO

File adapter for MRMFeatureQC files. More...

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

Inheritance diagram for MRMFeatureQCFile:

## Public Member Functions

| MRMFeatureQCFile ()=default
| Default constructor. More...
| ~MRMFeatureQCFile ()=default
| Destructor. More...
void | load (const String &filename, MRMFeatureQC &mrmfqc, const bool is_component_group) const
| Loads an MRMFeatureQC file. 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...

## Protected Member Functions

void | pushValuesFromLine_ (const StringList &line, const std::map< String, Size > &headers, std::vector< MRMFeatureQC::ComponentQCs > &c_qcs) const
| Save values from a line to a `ComponentQCs`. More...
void | pushValuesFromLine_ (const StringList &line, const std::map< String, Size > &headers, std::vector< MRMFeatureQC::ComponentGroupQCs > &cg_qcs) const
| Save values from a line to a `ComponentGroupQCs`. More...
void | setPairValue_ (const String &key, const String &value, const String &boundary, std::map< String, std::pair< double, double >> &meta_values_qc) const
| Set one of the values in a pair. More...
Int | getCastValue_ (const std::map< String, Size > &headers, const StringList &line, const String &header, const Int default_value) const
| Extracts a column's value from a line. More...
double | getCastValue_ (const std::map< String, Size > &headers, const StringList &line, const String &header, const double default_value) const
| Extracts a column's value from a line. More...
String | getCastValue_ (const std::map< String, Size > &headers, const StringList &line, const String &header, const String &default_value) const
| Extracts a column's value from a line. More...

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
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 ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_
Private 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...

## Detailed Description

File adapter for MRMFeatureQC files.

Loads and stores .csv or .tsv files describing an MRMFeatureQC.

## Constructor & Destructor Documentation

## ◆ MRMFeatureQCFile()

MRMFeatureQCFile | ( |  | ) |

default

Default constructor.

## ◆ ~MRMFeatureQCFile()

~MRMFeatureQCFile | ( |  | ) |

default

Destructor.

## Member Function Documentation

## ◆ getCastValue_() [1/3]

Int getCastValue_ | ( | const std::map< String, Size > & | headers,
|  | const StringList & | line,
|  | const String & | header,
|  | const Int | default_value
| ) |  | const

protected

Extracts a column's value from a line.

The method looks for the value found within `line[headers[header]]`. If the information is present and its value is valid, it will be converted to `Int` and returned. Otherwise, `default_value` (provided by the user) is returned.

Parameters

  [in] | headers | The mapping from columns' name to positions' indices
  [in] | line | A list of strings containing a single row's values
  [in] | header | The desired value's column name
  [in] | default_value | A default value to return in case the information is not found or invalid

Returns
  The found information (if found and valid) converted to `Int`. Otherwise `default_value`.

## ◆ getCastValue_() [2/3]

double getCastValue_ | ( | const std::map< String, Size > & | headers,
|  | const StringList & | line,
|  | const String & | header,
|  | const double | default_value
| ) |  | const

protected

Extracts a column's value from a line.

The method looks for the value found within `line[headers[header]]`. If the information is present and its value is valid, it will be converted to `double` and returned. Otherwise, `default_value` (provided by the user) is returned.

Parameters

  [in] | headers | The mapping from columns' name to positions' indices
  [in] | line | A list of strings containing a single row's values
  [in] | header | The desired value's column name
  [in] | default_value | A default value to return in case the information is not found or invalid

Returns
  The found information (if found and valid) converted to `double`. Otherwise `default_value`.

## ◆ getCastValue_() [3/3]

String getCastValue_ | ( | const std::map< String, Size > & | headers,
|  | const StringList & | line,
|  | const String & | header,
|  | const String & | default_value
| ) |  | const

protected

Extracts a column's value from a line.

The method looks for the value found within `line[headers[header]]`. If the information is present and its value is valid, it will be converted to `String` and returned. Otherwise, `default_value` (provided by the user) is returned.

Parameters

  [in] | headers | The mapping from columns' name to positions' indices
  [in] | line | A list of strings containing a single row's values
  [in] | header | The desired value's column name
  [in] | default_value | A default value to return in case the information is not found or invalid

Returns
  The found information (if found and valid) converted to `String`. Otherwise `default_value`.

## ◆ load()

void load | ( | const String & | filename,
|  | MRMFeatureQC & | mrmfqc,
|  | const bool | is_component_group
| ) |  | const

Loads an MRMFeatureQC file.

Exceptions

  Exception::FileNotFound | is thrown if the file could not be opened
  Exception::ParseError | is thrown if an error occurs during parsing

Parameters

  [in] | filename | The path to the input file
  [in,out] | mrmfqc | The output class which will contain the criteria
  [in] | is_component_group | true if the user intends to load ComponentGroupQCs data, false otherwise

## ◆ pushValuesFromLine_() [1/2]

void pushValuesFromLine_ | ( | const StringList & | line,
|  | const std::map< String, Size > & | headers,
|  | std::vector< MRMFeatureQC::ComponentQCs > & | c_qcs
| ) |  | const

protected

Save values from a line to a `ComponentQCs`.

Note
  Lines missing the `component_name` value will be skipped.

Parameters

  [in] | line | A line containing the values from a row in the input file
  [in] | headers | A mapping from headers names to position indices
  [out] | c_qcs | The output will be saved in a new element of this vector

## ◆ pushValuesFromLine_() [2/2]

void pushValuesFromLine_ | ( | const StringList & | line,
|  | const std::map< String, Size > & | headers,
|  | std::vector< MRMFeatureQC::ComponentGroupQCs > & | cg_qcs
| ) |  | const

protected

Save values from a line to a `ComponentGroupQCs`.

Note
  Lines missing the `component_group_name` value will be skipped.

Parameters

  [in] | line | A line containing the values from a row in the input file
  [in] | headers | A mapping from headers names to position indices
  [out] | cg_qcs | The output will be saved in a new element of this vector

## ◆ setPairValue_()

void setPairValue_ | ( | const String & | key,
|  | const String & | value,
|  | const String & | boundary,
|  | std::map< String, std::pair< double, double >> & | meta_values_qc
| ) |  | const

protected

Set one of the values in a pair.

The method is given in input a map from Strings to pairs. Assuming the key is present within the map, its mapped value will be updated with the given `value`, in the correct `boundary` position. If the key is not found, a new pair will be created and both its values set (in this case, a default value of 0.0 is given to the other pair's element).

Parameters

  [in] | key | The metavalue name
  [in] | value | The mapped pair
  [in] | boundary | "l" for lower bound or "u" for upper bound
  [out] | meta_values_qc | The map containing the metavalues and pairs