Base class for all map-alignment algorithms. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.h>
Public Member Functions | |
MapAlignmentAlgorithm () | |
Default constructor. More... | |
virtual | ~MapAlignmentAlgorithm () |
Destructor. More... | |
virtual void | alignPeakMaps (std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &) |
Aligns peak maps. More... | |
virtual void | alignCompactFeatureMaps (std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &) |
Aligns vectors of 2D peaks (memory efficient version of FeatureMap) More... | |
virtual void | alignFeatureMaps (std::vector< FeatureMap > &, std::vector< TransformationDescription > &) |
Aligns feature maps. More... | |
virtual void | alignConsensusMaps (std::vector< ConsensusMap > &, std::vector< TransformationDescription > &) |
Aligns consensus maps. More... | |
virtual void | alignPeptideIdentifications (std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &) |
Aligns peptide identifications. More... | |
virtual void | setReference (Size reference_index=0, const String &reference_file="") |
Defines a 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... | |
Static Public Member Functions | |
static void | fitModel (const String &model_type, const Param ¶ms, std::vector< TransformationDescription > &trafos) |
Fits a model with given parameters to the transformations. More... | |
static void | registerChildren () |
Register all derived classes in this method. More... | |
Private Member Functions | |
MapAlignmentAlgorithm (const MapAlignmentAlgorithm &) | |
Copy constructor is not implemented -> private. More... | |
MapAlignmentAlgorithm & | operator= (const MapAlignmentAlgorithm &) |
Assignment operator is not implemented -> private. More... | |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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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... | |
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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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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_ |
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static int | recursion_depth_ |
Base class for all map-alignment algorithms.
It takes two or more maps and corrects for retention time distortions.
The input maps are transformed and the transformation description is returned.
Default constructor.
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virtual |
Destructor.
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private |
Copy constructor is not implemented -> private.
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virtual |
Aligns vectors of 2D peaks (memory efficient version of FeatureMap)
Exception::NotImplemented | is thrown if an algorithm cannot align feature maps |
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virtual |
Aligns consensus maps.
Exception::NotImplemented | is thrown if an algorithm cannot align consensus maps |
Reimplemented in MapAlignmentAlgorithmIdentification.
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virtual |
Aligns feature maps.
Exception::NotImplemented | is thrown if an algorithm cannot align feature maps |
Reimplemented in MapAlignmentAlgorithmIdentification.
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virtual |
Aligns peak maps.
Exception::NotImplemented | is thrown if an algorithm cannot align peak maps |
Reimplemented in MapAlignmentAlgorithmIdentification, and MapAlignmentAlgorithmSpectrumAlignment.
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virtual |
Aligns peptide identifications.
Exception::NotImplemented | is thrown if an algorithm cannot align peptide identifications |
Reimplemented in MapAlignmentAlgorithmIdentification.
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static |
Fits a model with given parameters to the transformations.
This will not alter transformations of reference files (transformation type "identity").
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private |
Assignment operator is not implemented -> private.
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static |
Register all derived classes in this method.
Defines a reference for the alignment.
reference_index | Index of input file to use as reference (1-based!) |
reference_file | Path to external reference file |
Exception::InvalidParameter | is thrown if the algorithm does not support references |
Reimplemented in MapAlignmentAlgorithmIdentification.
OpenMS / TOPP release 2.0.0 | Documentation generated on Sat May 16 2015 16:13:55 using doxygen 1.8.9.1 |