OpenMS
2.6.0
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The base class of all element group finding algorithms. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>
Public Member Functions | |
BaseGroupFinder () | |
Default constructor. More... | |
~BaseGroupFinder () override | |
Destructor. More... | |
virtual void | run (const std::vector< ConsensusMap > &input, ConsensusMap &result)=0 |
Run the algorithm. More... | |
Public Member Functions inherited from DefaultParamHandler | |
DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. 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 | registerChildren () |
Register all derived classes here. More... | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") |
Writes all parameters to meta values. More... | |
Protected Member Functions | |
void | checkIds_ (const std::vector< ConsensusMap > &maps) const |
Checks if all file descriptions have disjoint map identifiers. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Private Member Functions | |
BaseGroupFinder (const BaseGroupFinder &) | |
Copy constructor intentionally not implemented. More... | |
BaseGroupFinder & | operator= (const BaseGroupFinder &) |
Assignment operator intentionally not implemented. 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 DefaultParamHandler | |
Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. 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_ |
The base class of all element group finding algorithms.
This class defines the basic interface for all element group finding algorithms.
All derived algorithms take one or several consensus maps and find corresponding features across the maps (or within one map). They return one consensus map containing the found consensus features.
The element indices of the result consensus features are the container access indices of the input maps. The map indices of the result consensus features are are the indices in the input map vector.
BaseGroupFinder | ( | ) |
Default constructor.
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override |
Destructor.
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private |
Copy constructor intentionally not implemented.
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protected |
Checks if all file descriptions have disjoint map identifiers.
Exception::IllegalArgument | Is thrown if a file id is found twice |
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private |
Assignment operator intentionally not implemented.
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static |
Register all derived classes here.
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pure virtual |
Run the algorithm.
Exception::IllegalArgument | is thrown if the input data is not valid. |
Implemented in QTClusterFinder, StablePairFinder, SimplePairFinder, and LabeledPairFinder.