OpenMS
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#include <OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h>
Classes | |
struct | AnnotatedHit_ |
Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space. More... | |
Public Types | |
enum class | ExitCodes { EXECUTION_OK , INPUT_FILE_EMPTY , UNEXPECTED_RESULT , UNKNOWN_ERROR , ILLEGAL_PARAMETERS } |
Exit codes. More... | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD , GUI , NONE } |
Possible log types. More... | |
Public Member Functions | |
SimpleSearchEngineAlgorithm () | |
ExitCodes | search (const String &in_mzML, const String &in_db, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids) const |
search spectra against database 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... | |
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... | |
virtual | ~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 | setLogger (ProgressLoggerImpl *logger) |
Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Protected Member Functions | |
void | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | postProcessHits_ (const PeakMap &exp, std::vector< std::vector< SimpleSearchEngineAlgorithm::AnnotatedHit_ > > &annotated_hits, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, Size top_hits, const ModifiedPeptideGenerator::MapToResidueType &fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType &variable_modifications, Size max_variable_mods_per_peptide, const StringList &modifications_fixed, const StringList &modifications_variable, Int peptide_missed_cleavages, double precursor_mass_tolerance, double fragment_mass_tolerance, const String &precursor_mass_tolerance_unit_ppm, const String &fragment_mass_tolerance_unit_ppm, const Int precursor_min_charge, const Int precursor_max_charge, const String &enzyme, const String &database_name) const |
filter and annotate search results most of the parameters are used to properly add meta data to the id objects 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 | |
static void | preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm) |
filter, deisotope, decharge spectra More... | |
Additional Inherited Members | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
Writes all parameters to meta values. More... | |
Static Protected Attributes inherited from ProgressLogger | |
static int | recursion_depth_ |
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filter and annotate search results most of the parameters are used to properly add meta data to the id objects
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filter, deisotope, decharge spectra
ExitCodes search | ( | const String & | in_mzML, |
const String & | in_db, | ||
std::vector< ProteinIdentification > & | prot_ids, | ||
std::vector< PeptideIdentification > & | pep_ids | ||
) | const |
search spectra against database
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overrideprotectedvirtual |
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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