This class implements different precursor ion selection strategies. More...
#include <OpenMS/ANALYSIS/TARGETED/PrecursorIonSelection.h>
Classes | |
struct | SeqTotalScoreMore |
Compare by score. More... | |
struct | TotalScoreMore |
Compare by score. More... | |
Public Types | |
enum | Type { IPS, ILP_IPS, SPS, UPSHIFT, DOWNSHIFT, DEX } |
Precursor ion selection type (iterative, static, upshift, downshift, dynamic exclusion). More... | |
Public Member Functions | |
PrecursorIonSelection () | |
PrecursorIonSelection (const PrecursorIonSelection &source) | |
~PrecursorIonSelection () | |
const double & | getMaxScore () const |
void | setMaxScore (const double &max_score) |
void | sortByTotalScore (FeatureMap &features) |
Sort features by total score. More... | |
void | getNextPrecursors (FeatureMap &features, FeatureMap &next_features, UInt number) |
Returns features with highest score for MS/MS. More... | |
void | getNextPrecursorsSeq (FeatureMap &features, FeatureMap &next_features, UInt number, double &rt) |
void | getNextPrecursors (std::vector< Int > &solution_indices, std::vector< PSLPFormulation::IndexTriple > &variable_indices, std::set< Int > &measured_variables, FeatureMap &features, FeatureMap &new_features, UInt step_size, PSLPFormulation &ilp) |
void | rescore (FeatureMap &features, std::vector< PeptideIdentification > &new_pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, bool check_meta_values=true) |
Change scoring of features using peptide identifications only from spectra of the last iteration. More... | |
void | simulateRun (FeatureMap &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, MSExperiment<> &experiment, String precursor_path="") |
Simulate the iterative precursor ion selection. More... | |
void | setLPSolver (LPWrapper::SOLVER solver) |
LPWrapper::SOLVER | getLPSolver () |
void | reset () |
const std::map< String, std::set< String > > & | getPeptideProteinCounter () |
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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... | |
Private Member Functions | |
void | simulateILPBasedIPSRun_ (FeatureMap &features, MSExperiment<> &experiment, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String output_path, String precursor_path="") |
void | simulateRun_ (FeatureMap &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, String precursor_path="") |
void | shiftDown_ (FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc) |
void | shiftUp_ (FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc) |
void | updateMembers_ () |
update members method from DefaultParamHandler to update the members More... | |
void | rescore_ (FeatureMap &features, std::vector< PeptideIdentification > &new_pep_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, PSProteinInference &protein_inference) |
void | checkForRequiredUserParams_ (FeatureMap &features) |
Adds user params, required for the use of IPS, to a feature map using default values. More... | |
UInt | filterProtIds_ (std::vector< ProteinIdentification > &prot_ids) |
Groups protein identifications that cannot be distinguished by their peptide identifications. More... | |
std::vector< PeptideIdentification > | filterPeptideIds_ (std::vector< PeptideIdentification > &pep_ids) |
void | convertPeptideIdScores_ (std::vector< PeptideIdentification > &pep_ids) |
Private Attributes | |
UInt | min_pep_ids_ |
minimal number of peptides identified for a protein to be declared identified More... | |
double | max_score_ |
maximal score in the FeatureMap More... | |
Type | type_ |
precursor ion selection strategy More... | |
std::map< String, std::set< String > > | prot_id_counter_ |
stores the peptide sequences for all protein identifications More... | |
std::vector< Size > | fraction_counter_ |
stores the number of selected precursors per fraction More... | |
double | mz_tolerance_ |
precursor ion error tolerance More... | |
String | mz_tolerance_unit_ |
precursor ion error tolerance unit (ppm or Da) More... | |
UInt | max_iteration_ |
maximal number of iterations More... | |
Size | x_variable_number_ |
LPWrapper::SOLVER | solver_ |
Additional Inherited Members | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
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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... | |
This class implements different precursor ion selection strategies.
enum Type |
Precursor ion selection type (iterative, static, upshift, downshift, dynamic exclusion).
The iterative strategy changes the ranking of possible precursors based on identification results from previous iterations.
The upshift strategy assigns a higher priority to precursors whose masses are matching peptide masses of potential protein identifications to enable a safe identification in the next iterations.
The downshift strategy assigns a lower priority to precursors whose masses are matching peptide masses of safe protein identifications.
The dynamic exclusion excludes precursors whose masses are matching peptide masses of safe protein identifications.
The static selection uses precomputed scores to rank the precursor, the order of precursors isn't changed throughout the run.
Enumerator | |
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IPS | |
ILP_IPS | |
SPS | |
UPSHIFT | |
DOWNSHIFT | |
DEX |
PrecursorIonSelection | ( | const PrecursorIonSelection & | source | ) |
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Adds user params, required for the use of IPS, to a feature map using default values.
features | FeatureMap with all possible precursors |
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Groups protein identifications that cannot be distinguished by their peptide identifications.
prot_ids | All protein identifications. |
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const double& getMaxScore | ( | ) | const |
void getNextPrecursors | ( | FeatureMap & | features, |
FeatureMap & | next_features, | ||
UInt | number | ||
) |
Returns features with highest score for MS/MS.
features | FeatureMap with all possible precursors |
next_features | FeatureMap with next precursors |
number | Number of features to be reported |
void getNextPrecursors | ( | std::vector< Int > & | solution_indices, |
std::vector< PSLPFormulation::IndexTriple > & | variable_indices, | ||
std::set< Int > & | measured_variables, | ||
FeatureMap & | features, | ||
FeatureMap & | new_features, | ||
UInt | step_size, | ||
PSLPFormulation & | ilp | ||
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void getNextPrecursorsSeq | ( | FeatureMap & | features, |
FeatureMap & | next_features, | ||
UInt | number, | ||
double & | rt | ||
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void rescore | ( | FeatureMap & | features, |
std::vector< PeptideIdentification > & | new_pep_ids, | ||
std::vector< ProteinIdentification > & | prot_ids, | ||
PrecursorIonSelectionPreprocessing & | preprocessed_db, | ||
bool | check_meta_values = true |
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) |
Change scoring of features using peptide identifications only from spectra of the last iteration.
features | FeatureMap with all possible precursors |
new_pep_ids | Peptide identifications |
preprocessed_db | Information from preprocessed database Change scoring of features using peptide identifications from all spectra. |
features | FeatureMap with all possible precursors |
new_pep_ids | Peptide identifications |
prot_ids | Protein identifications |
preprocessed_db | Information from preprocessed database |
check_meta_values | True if the FeatureMap should be checked for the presence of required meta values |
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void reset | ( | ) |
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void setMaxScore | ( | const double & | max_score | ) |
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void simulateRun | ( | FeatureMap & | features, |
std::vector< PeptideIdentification > & | pep_ids, | ||
std::vector< ProteinIdentification > & | prot_ids, | ||
PrecursorIonSelectionPreprocessing & | preprocessed_db, | ||
String | path, | ||
MSExperiment<> & | experiment, | ||
String | precursor_path = "" |
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) |
Simulate the iterative precursor ion selection.
features | FeatureMap with all possible precursors |
pep_ids | Peptide identifications |
prot_ids | Protein identifications |
preprocessed_db | Information from preprocessed database |
step_size | Number of MS/MS spectra considered per iteration |
path | Path to output file |
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Sort features by total score.
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privatevirtual |
update members method from DefaultParamHandler to update the members
Reimplemented from DefaultParamHandler.
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stores the number of selected precursors per fraction
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maximal number of iterations
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maximal score in the FeatureMap
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minimal number of peptides identified for a protein to be declared identified
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precursor ion error tolerance
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precursor ion error tolerance unit (ppm or Da)
stores the peptide sequences for all protein identifications
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precursor ion selection strategy
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OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |