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OpenMS
2.4.0
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A map alignment algorithm based on pose clustering. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmPoseClustering.h>
Public Member Functions | |
MapAlignmentAlgorithmPoseClustering () | |
Default constructor. More... | |
~MapAlignmentAlgorithmPoseClustering () override | |
Destructor. More... | |
void | align (const FeatureMap &map, TransformationDescription &trafo) |
void | align (const PeakMap &map, TransformationDescription &trafo) |
void | align (const ConsensusMap &map, TransformationDescription &trafo) |
template<typename MapType > | |
void | setReference (const MapType &map) |
Sets the reference for the alignment. More... | |
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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... | |
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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 | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
PoseClusteringAffineSuperimposer | superimposer_ |
StablePairFinder | pairfinder_ |
ConsensusMap | reference_ |
Int | max_num_peaks_considered_ |
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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... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Private Member Functions | |
MapAlignmentAlgorithmPoseClustering (const MapAlignmentAlgorithmPoseClustering &) | |
Copy constructor intentionally not implemented -> private. More... | |
MapAlignmentAlgorithmPoseClustering & | operator= (const MapAlignmentAlgorithmPoseClustering &) |
Assignment operator intentionally not implemented -> private. More... | |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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static int | recursion_depth_ |
A map alignment algorithm based on pose clustering.
Pose clustering analyzes pair distances to find the most probable transformation of retention times.
The algorithm chooses the x most intensity peaks/features per map. This is modeled via the parameter 'max_num_peaks_considered', which in turn influences the runtime and stability of the results. Bigger values prolong computation, smaller values might lead to no or unstable trafos. Set to -1 to use all features (might take very long for large maps).
For further details see:
Eva Lange et al.
A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data
ISMB/ECCB 2007
Default constructor.
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override |
Destructor.
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private |
Copy constructor intentionally not implemented -> private.
void align | ( | const ConsensusMap & | map, |
TransformationDescription & | trafo | ||
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void align | ( | const FeatureMap & | map, |
TransformationDescription & | trafo | ||
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void align | ( | const PeakMap & | map, |
TransformationDescription & | trafo | ||
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private |
Assignment operator intentionally not implemented -> private.
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inline |
Sets the reference for the alignment.
References MapConversion::convert().
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overrideprotectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
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