OpenMS  2.8.0
Classes | Public Types | Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
SimpleSearchEngineAlgorithm Class Reference

#include <OpenMS/ANALYSIS/ID/SimpleSearchEngineAlgorithm.h>

Inheritance diagram for SimpleSearchEngineAlgorithm:
Collaboration diagram for SimpleSearchEngineAlgorithm:


struct  AnnotatedHit_
 Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space. More...

Public Types

enum class  ExitCodes {
 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...
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
void setParameters (const Param &param)
 Sets the parameters. More...
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
const StringgetName () 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...
ProgressLoggeroperator= (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...

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...
- 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

double precursor_mass_tolerance_
String precursor_mass_tolerance_unit_
Size precursor_min_charge_
Size precursor_max_charge_
IntList precursor_isotopes_
double fragment_mass_tolerance_
String fragment_mass_tolerance_unit_
StringList modifications_fixed_
StringList modifications_variable_
Size modifications_max_variable_mods_per_peptide_
String enzyme_
bool decoys_
StringList annotate_psm_
Size peptide_min_size_
Size peptide_max_size_
Size peptide_missed_cleavages_
String peptide_motif_
Size report_top_hits_
- 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< Stringsubsections_
 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_

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_

Member Enumeration Documentation

◆ ExitCodes

enum ExitCodes

Exit codes.


Constructor & Destructor Documentation

◆ SimpleSearchEngineAlgorithm()

Member Function Documentation

◆ postProcessHits_()

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

◆ preprocessSpectra_()

static void preprocessSpectra_ ( PeakMap exp,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm 

filter, deisotope, decharge spectra

◆ search()

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

◆ updateMembers_()

void updateMembers_ ( )

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.

Member Data Documentation

◆ annotate_psm_

StringList annotate_psm_

◆ decoys_

bool decoys_

◆ enzyme_

String enzyme_

◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

◆ fragment_mass_tolerance_unit_

String fragment_mass_tolerance_unit_

◆ modifications_fixed_

StringList modifications_fixed_

◆ modifications_max_variable_mods_per_peptide_

Size modifications_max_variable_mods_per_peptide_

◆ modifications_variable_

StringList modifications_variable_

◆ peptide_max_size_

Size peptide_max_size_

◆ peptide_min_size_

Size peptide_min_size_

◆ peptide_missed_cleavages_

Size peptide_missed_cleavages_

◆ peptide_motif_

String peptide_motif_

◆ precursor_isotopes_

IntList precursor_isotopes_

◆ precursor_mass_tolerance_

double precursor_mass_tolerance_

◆ precursor_mass_tolerance_unit_

String precursor_mass_tolerance_unit_

◆ precursor_max_charge_

Size precursor_max_charge_

◆ precursor_min_charge_

Size precursor_min_charge_

◆ report_top_hits_

Size report_top_hits_