#include <OpenMS/ANALYSIS/ID/AccurateMassSearchEngine.h>
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 &) |
![]() | |
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... | |
![]() | |
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... | |
![]() | |
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< DoubleReal > | masskey_table_ |
MassIDMapping | mass_id_mapping_ |
HMDBPropsMapping | hmdb_properties_mapping_ |
std::vector< String > | mass_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 | |
![]() | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
![]() | |
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... | |
![]() | |
LogType | type_ |
SignedSize | begin_ |
SignedSize | end_ |
SignedSize | value_ |
QProgressDialog * | dlg_ |
StopWatch | stop_watch_ |
time_t | last_invoke_ |
![]() | |
static int | recursion_depth_ |
|
private |
|
private |
private member variables
|
private |
Default constructor.
|
virtual |
Default destructor.
|
private |
|
private |
|
private |
|
private |
|
private |
|
private |
|
private |
private member functions
|
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 & | |||
) |
|
private |
|
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.
|
private |
|
private |
|
private |
|
private |
|
private |
parameter stuff
|
private |
|
private |
|
private |
|
private |
|
private |
|
private |
|
private |
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |