OpenMS
2.5.0
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#include <OpenMS/ANALYSIS/XLMS/XFDRAlgorithm.h>
Public Types | |
enum | ExitCodes { EXECUTION_OK, ILLEGAL_PARAMETERS, UNEXPECTED_RESULT } |
Exit codes. More... | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Public Member Functions | |
XFDRAlgorithm () | |
Default constructor. More... | |
~XFDRAlgorithm () override | |
Default destructor. More... | |
ExitCodes | run (std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id) |
Performs the main function of this class, the FDR estimation for cross-linked peptide experiments. More... | |
ExitCodes | validateClassArguments () const |
Checks whether the parameters of the object are valid. 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... | |
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 | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | initDataStructures_ (std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id) |
Prepares vector of PeptideIdentification such that it can be processed downstream. The encompassed steps are: * Set min_score_ and max_score_ encountered in the data * Ensure that crosslink_type and crosslink_rank are available in the PeptideIdentification * Define the crosslink as either inter/or intraprotein * Set the identifier of the Peptide Identification if there is only one protein identification. More... | |
void | fdr_xprophet_ (std::map< String, Math::Histogram<> > &cum_histograms, const String &targetclass, const String &decoyclass, const String &fulldecoyclass, std::vector< double > &fdr, bool mono) |
xprophet method for target hits counting as implemented in xProphet More... | |
void | findTopUniqueHits_ (std::vector< PeptideIdentification > &peptide_ids) |
void | writeArgumentsLog_ () const |
String | getId_ (const PeptideHit &ph) const |
Static Private Member Functions | |
static void | assignTypes_ (PeptideHit &ph, StringList &types) |
Inspects PeptideIdentification pep_id and assigns all cross-link types that this identification belongs to. More... | |
static void | calc_qfdr_ (const std::vector< double > &fdr, std::vector< double > &qfdr) |
Calculates the qFDR values for the provided FDR values, assuming that the FDRs are sorted by score in the input vector. More... | |
static Size | getMinIonsMatched_ (const PeptideHit &ph) |
static void | setIntraProtein_ (PeptideHit &ph, const bool value) |
static void | setInterProtein_ (PeptideHit &ph, const bool value) |
static bool | isSameProtein_ (String prot1, String prot2, const String &decoy_string) |
Determines whether the Petide Evidences belong to the same protein, modulo decoy. More... | |
Private Attributes | |
Int | min_score_ |
Int | max_score_ |
std::vector< String > | unique_ids_ |
std::vector< double > | unique_id_scores_ |
std::map< String, std::vector< String > > | cross_link_classes_ |
String | decoy_string_ |
double | arg_mindeltas_ |
double | arg_minborder_ |
double | arg_maxborder_ |
Int | arg_minionsmatched_ |
double | arg_minscore_ |
bool | arg_uniquex_ |
bool | arg_no_qvalues_ |
double | arg_binsize_ |
Static Private Attributes | |
static const String | param_decoy_string_ |
static const String | param_minborder_ |
static const String | param_maxborder_ |
static const String | param_mindeltas_ |
static const String | param_minionsmatched_ |
static const String | param_uniquexl_ |
static const String | param_no_qvalues_ |
static const String | param_minscore_ |
static const String | param_binsize_ |
static const String | crosslink_class_intradecoys_ |
static const String | crosslink_class_fulldecoysintralinks_ |
static const String | crosslink_class_interdecoys_ |
static const String | crosslink_class_fulldecoysinterlinks_ |
static const String | crosslink_class_monodecoys_ |
static const String | crosslink_class_intralinks_ |
static const String | crosslink_class_interlinks_ |
static const String | crosslink_class_monolinks_ |
static const String | crosslink_class_decoys_ |
static const String | crosslink_class_targets_ |
static const String | crosslink_class_hybriddecoysintralinks_ |
static const String | crosslink_class_hybriddecoysinterlinks_ |
Additional Inherited Members | |
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_ |
enum ExitCodes |
XFDRAlgorithm | ( | ) |
Default constructor.
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override |
Default destructor.
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staticprivate |
Inspects PeptideIdentification pep_id and assigns all cross-link types that this identification belongs to.
pep_id | Peptide ID to be assigned. |
types | Result vector containing the names of the crosslink classes |
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staticprivate |
Calculates the qFDR values for the provided FDR values, assuming that the FDRs are sorted by score in the input vector.
fdr | Vector with FDR values which should be used for qFDR calculation |
qfdr | Result qFDR values |
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xprophet method for target hits counting as implemented in xProphet
Target counting as performed by the xProphet software package
cum_histograms | Cumulative score distributions |
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inlinestaticprivate |
References MetaInfoInterface::getMetaValue().
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Prepares vector of PeptideIdentification such that it can be processed downstream. The encompassed steps are: * Set min_score_ and max_score_ encountered in the data * Ensure that crosslink_type and crosslink_rank are available in the PeptideIdentification * Define the crosslink as either inter/or intraprotein * Set the identifier of the Peptide Identification if there is only one protein identification.
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inlinestaticprivate |
Determines whether the Petide Evidences belong to the same protein, modulo decoy.
References String::hasSubstring(), and String::substitute().
ExitCodes run | ( | std::vector< PeptideIdentification > & | peptide_ids, |
ProteinIdentification & | protein_id | ||
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Performs the main function of this class, the FDR estimation for cross-linked peptide experiments.
peptide_ids | The PeptideIdentifications from an XL-MS experiment |
Referenced by TOPPXFDR::main_().
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inlinestaticprivate |
References MetaInfoInterface::setMetaValue().
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inlinestaticprivate |
References MetaInfoInterface::setMetaValue().
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overrideprivatevirtual |
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.
ExitCodes validateClassArguments | ( | ) | const |
Checks whether the parameters of the object are valid.
Referenced by TOPPXFDR::main_().
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