| OpenMS 2.5.0

Public Member Functions | Protected Attributes | List of all members
FeatureFinder Class Reference
Analysis » FeatureFinder

The main feature finder class. More...

`#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h>`

Inheritance diagram for FeatureFinder:

## Public Member Functions

| FeatureFinder ()
| Default constructor. More...
virtual | ~FeatureFinder ()
| Destructor. More...
void | run (const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param &param, const FeatureMap &seeds)
| Executes the FeatureFinder using the given algorithm. More...
const Flag & | getPeakFlag (const IndexPair &index) const
| Returns a non-mutable reference to a peak flag. More...
Flag & | getPeakFlag (const IndexPair &index)
| Returns mutable reference to a peak flag. More...
Param | getParameters (const String &algorithm_name) const
| Returns the default parameters for the algorithm with name `algorithm_name`. 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 Attributes

std::vector< std::vector< Flag > > | flags_
| Container for flags attached to input data. More...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
Public Types inherited from FeatureFinderDefs
enum | Flag { UNUSED, USED }
| Flags that indicate if a peak is already used in a feature. More...
typedef IsotopeCluster::IndexPair | IndexPair
| Index to peak consisting of two UInts (scan index / peak index) More...
typedef IsotopeCluster::ChargedIndexSet | ChargedIndexSet
| Index to peak consisting of two UInts (scan index / peak index) with charge information. More...
typedef IsotopeCluster::IndexSet | IndexSet
| A set of peak indices. 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...
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

The main feature finder class.

- Stores the flags for (indices of) data points ("used", "unused")
- The algorithm itself is a factory product (derived from FeatureFinderAlgorithm)
- The main method is run(), which is a template so that we can deal with different types of input and output
- The run() method takes five arguments: algorithm_name, input_map, output, parameters, seeds

## Constructor & Destructor Documentation

## ◆ FeatureFinder()

FeatureFinder | ( |  | ) |

Default constructor.

## ◆ ~FeatureFinder()

virtual ~FeatureFinder | ( |  | ) |

virtual

Destructor.

## Member Function Documentation

## ◆ getParameters()

Param getParameters | ( | const String & | algorithm_name | ) | const

Returns the default parameters for the algorithm with name `algorithm_name`.

## ◆ getPeakFlag() [1/2]

const Flag& getPeakFlag | ( | const IndexPair & | index | ) | const

inline

Returns a non-mutable reference to a peak flag.

## ◆ getPeakFlag() [2/2]

Flag& getPeakFlag | ( | const IndexPair & | index | ) |

inline

Returns mutable reference to a peak flag.

## ◆ run()

void run | ( | const String & | algorithm_name,
|  | PeakMap & | input_map,
|  | FeatureMap & | features,
|  | const Param & | param,
|  | const FeatureMap & | seeds
| ) |  |

Executes the FeatureFinder using the given algorithm.

There are several constraints for the `input_map`. They are tested before the algorithm starts. It must only contain MS 1 level scans and you have to call updateRanges() before passing it to this method. The input map is sorted by RT & m/z if that's not the case. Furthermore we throw an Exception if the data contains negative m/z values, as this will disturb most algorithms.

Parameters

  algorithm_name | Name of the feature finding algorithm to use
  input_map | Input peak map
  features | Output feature map
  param | Algorithm parameters
  seeds | List of seeds to use

Implemented in FeatureFinder_impl.h

## Member Data Documentation

## ◆ flags_

std::vector<std::vector<Flag> > flags_

protected

Container for flags attached to input data.