OpenMS
2.6.0
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Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental). More...
#include <OpenMS/ANALYSIS/ID/BayesianProteinInferenceAlgorithm.h>
Public Member Functions | |
BayesianProteinInferenceAlgorithm (unsigned int debug_lvl=0) | |
Constructor. More... | |
~BayesianProteinInferenceAlgorithm () override=default | |
Destructor. More... | |
void | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | inferPosteriorProbabilities (std::vector< ProteinIdentification > &proteinIDs, std::vector< PeptideIdentification > &peptideIDs, boost::optional< const ExperimentalDesign > exp_des=boost::optional< const ExperimentalDesign >()) |
void | inferPosteriorProbabilities (ConsensusMap &cmap, bool greedy_group_resolution, boost::optional< const ExperimentalDesign > exp_des=boost::optional< const ExperimentalDesign >()) |
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... | |
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... | |
Private Member Functions | |
void | inferPosteriorProbabilities_ (Internal::IDBoostGraph &ibg) |
GridSearch< double, double, double > | initGridSearchFromParams_ (std::vector< double > &alpha_search, std::vector< double > &beta_search, std::vector< double > &gamma_search) |
read Param object and set the grid More... | |
void | setScoreTypeAndSettings_ (ProteinIdentification &proteinIDs) |
set score type and settings for every ProteinID run processed More... | |
void | resetProteinScores_ (ProteinIdentification &protein_id, bool keep_old_as_prior) |
reset all protein scores to 0.0, save old ones as Prior MetaValue if requested More... | |
Private Attributes | |
std::function< void(PeptideIdentification &)> | checkConvertAndFilterPepHits_ |
unsigned int | debug_lvl_ |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") |
Writes all parameters to meta values. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Static Protected Member Functions inherited from ProgressLogger | |
static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. 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_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Static Protected Attributes inherited from ProgressLogger | |
static int | recursion_depth_ |
Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental).
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explicit |
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overridedefault |
Destructor.
void inferPosteriorProbabilities | ( | ConsensusMap & | cmap, |
bool | greedy_group_resolution, | ||
boost::optional< const ExperimentalDesign > | exp_des = boost::optional< const ExperimentalDesign >() |
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Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function. Writes its results into protein and (optionally also) peptide hits (as new score). Optionally adds indistinguishable protein groups with separate scores, too. See Param object of class. Loops over all runs in the ConsensusMaps' protein IDs. (experimental)
void inferPosteriorProbabilities | ( | std::vector< ProteinIdentification > & | proteinIDs, |
std::vector< PeptideIdentification > & | peptideIDs, | ||
boost::optional< const ExperimentalDesign > | exp_des = boost::optional< const ExperimentalDesign >() |
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) |
Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function. Writes its results into protein and (optionally also) peptide hits (as new score). Optionally adds indistinguishable protein groups with separate scores, too. See Param object of class. Currently only takes first proteinID run and all peptides. Experimental design can be used to create an extended graph with replicate information. (experimental) @TODO loop over all runs
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private |
after a graph was built, use this method to perform inference and write results to the structures with which the graph was built
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private |
read Param object and set the grid
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private |
reset all protein scores to 0.0, save old ones as Prior MetaValue if requested
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set score type and settings for every ProteinID run processed
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overridevirtual |
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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private |
function initialized based on the algorithm parameters that is used to filter PeptideHits
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private |