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... | |
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... | |
| 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 | |
Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. 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... | |
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_ |
| SignedSize | begin_ |
| SignedSize | end_ |
| SignedSize | value_ |
| QProgressDialog * | dlg_ |
| StopWatch | stop_watch_ |
| time_t | last_invoke_ |
Static Protected Attributes inherited from ProgressLogger | |
| 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.
|
virtual |
Destructor.
|
private |
Copy constructor is not implemented -> private.
|
virtual |
Aligns vectors of 2D peaks (memory efficient version of FeatureMap)
| Exception::NotImplemented | is thrown if an algorithm cannot align feature maps |
|
virtual |
Aligns consensus maps.
| Exception::NotImplemented | is thrown if an algorithm cannot align consensus maps |
Reimplemented in MapAlignmentAlgorithmIdentification.
|
virtual |
Aligns feature maps.
| Exception::NotImplemented | is thrown if an algorithm cannot align feature maps |
Reimplemented in MapAlignmentAlgorithmIdentification.
|
virtual |
Aligns peak maps.
| Exception::NotImplemented | is thrown if an algorithm cannot align peak maps |
Reimplemented in MapAlignmentAlgorithmIdentification, and MapAlignmentAlgorithmSpectrumAlignment.
|
virtual |
Aligns peptide identifications.
| Exception::NotImplemented | is thrown if an algorithm cannot align peptide identifications |
Reimplemented in MapAlignmentAlgorithmIdentification.
|
static |
Fits a model with given parameters to the transformations.
This will not alter transformations of reference files (transformation type "identity").
|
private |
Assignment operator is not implemented -> private.
|
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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |