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AccurateMassSearchEngine Class Reference

#include <OpenMS/ANALYSIS/ID/AccurateMassSearchEngine.h>

Inheritance diagram for AccurateMassSearchEngine:
DefaultParamHandler ProgressLogger

Public Member Functions

 AccurateMassSearchEngine ()
 Default constructor. More...
 
virtual ~AccurateMassSearchEngine ()
 Default destructor. More...
 
void queryByMass (const DoubleReal &, const DoubleReal &, std::vector< AccurateMassSearchResult > &)
 
void queryByFeature (const Feature &, const Size &, std::vector< AccurateMassSearchResult > &)
 
void queryByConsensusFeature (const ConsensusFeature &, const Size &, const Size &, std::vector< AccurateMassSearchResult > &)
 
void run (const FeatureMap<> &, MzTab &)
 main method of AccurateMassSearchEngine More...
 
void run (const ConsensusMap &, MzTab &)
 
- 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 

Protected Member Functions

virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Private Types

typedef std::vector
< std::vector
< AccurateMassSearchResult > > 
QueryResultsTable
 
typedef std::vector
< std::vector< String > > 
MassIDMapping
 private member variables More...
 
typedef std::map< String,
std::vector< String > > 
HMDBPropsMapping
 

Private Member Functions

void parseMappingFile_ (const String &)
 private member functions More...
 
void parseStructMappingFile_ (const String &)
 
void parseAdductsFile_ (const String &)
 
void searchMass_ (const DoubleReal &, std::vector< Size > &hit_indices)
 
void parseAdductString_ (const String &, std::vector< String > &)
 
void computeNeutralMassFromAdduct_ (const DoubleReal &, const String &, DoubleReal &, DoubleReal &)
 
DoubleReal computeCosineSim_ (const std::vector< DoubleReal > &x, const std::vector< DoubleReal > &y)
 
DoubleReal computeEuclideanDist_ (const std::vector< DoubleReal > &x, const std::vector< DoubleReal > &y)
 
DoubleReal computeIsotopePatternSimilarity_ (const Feature &, const EmpiricalFormula &)
 
void exportMzTab_ (const QueryResultsTable &, MzTab &)
 

Private Attributes

std::vector< DoubleRealmasskey_table_
 
MassIDMapping mass_id_mapping_
 
HMDBPropsMapping hmdb_properties_mapping_
 
std::vector< Stringmass_formula_mapping_
 
DoubleReal mass_error_value_
 parameter stuff More...
 
String mass_error_unit_
 
String ion_mode_
 
bool iso_similarity_
 
String pos_adducts_fname_
 
String neg_adducts_fname_
 
StringList pos_adducts_
 
StringList neg_adducts_
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. 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< Stringsubsections_
 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_
 

Member Typedef Documentation

typedef std::map<String, std::vector<String> > HMDBPropsMapping
private
typedef std::vector<std::vector<String> > MassIDMapping
private

private member variables

typedef std::vector<std::vector<AccurateMassSearchResult> > QueryResultsTable
private

Constructor & Destructor Documentation

Default constructor.

virtual ~AccurateMassSearchEngine ( )
virtual

Default destructor.

Member Function Documentation

DoubleReal computeCosineSim_ ( const std::vector< DoubleReal > &  x,
const std::vector< DoubleReal > &  y 
)
private
DoubleReal computeEuclideanDist_ ( const std::vector< DoubleReal > &  x,
const std::vector< DoubleReal > &  y 
)
private
DoubleReal computeIsotopePatternSimilarity_ ( const Feature ,
const EmpiricalFormula  
)
private
void computeNeutralMassFromAdduct_ ( const DoubleReal ,
const String ,
DoubleReal ,
DoubleReal  
)
private
void exportMzTab_ ( const QueryResultsTable ,
MzTab  
)
private
void parseAdductsFile_ ( const String )
private
void parseAdductString_ ( const String ,
std::vector< String > &   
)
private
void parseMappingFile_ ( const String )
private

private member functions

void parseStructMappingFile_ ( const String )
private
void queryByConsensusFeature ( const ConsensusFeature ,
const Size ,
const Size ,
std::vector< AccurateMassSearchResult > &   
)
void queryByFeature ( const Feature ,
const Size ,
std::vector< AccurateMassSearchResult > &   
)
void queryByMass ( const DoubleReal ,
const DoubleReal ,
std::vector< AccurateMassSearchResult > &   
)
void run ( const FeatureMap<> &  ,
MzTab  
)

main method of AccurateMassSearchEngine

void run ( const ConsensusMap ,
MzTab  
)
void searchMass_ ( const DoubleReal ,
std::vector< Size > &  hit_indices 
)
private
virtual void updateMembers_ ( )
protectedvirtual

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.

Member Data Documentation

HMDBPropsMapping hmdb_properties_mapping_
private
String ion_mode_
private
bool iso_similarity_
private
String mass_error_unit_
private
DoubleReal mass_error_value_
private

parameter stuff

std::vector<String> mass_formula_mapping_
private
MassIDMapping mass_id_mapping_
private
std::vector<DoubleReal> masskey_table_
private
StringList neg_adducts_
private
String neg_adducts_fname_
private
StringList pos_adducts_
private
String pos_adducts_fname_
private

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5