| OpenMS 2.5.0

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:

## Classes

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

## Public Types

enum | 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...
virtual DefaultParamHandler & | operator= (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 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...

## Protected Member Functions

void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. 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 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)
| filter and annotate search results most of the parameters are used to properly add meta data to the id objects 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_
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< 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_

## Additional Inherited Members

Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Member Enumeration Documentation

## ◆ ExitCodes

enum ExitCodes

strong

Exit codes.

Enumerator
EXECUTION_OK |
INPUT_FILE_EMPTY |
UNEXPECTED_RESULT |
UNKNOWN_ERROR |
ILLEGAL_PARAMETERS |

## Constructor & Destructor Documentation

## ◆ SimpleSearchEngineAlgorithm()

SimpleSearchEngineAlgorithm | ( |  | ) |

## Member Function Documentation

## ◆ postProcessHits_()

static 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
| ) |  |

static protected

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
| ) |  |

static protected

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_ | ( |  | ) |

override protected virtual

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

## ◆ enzyme_

String enzyme_

protected

## ◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

## ◆ fragment_mass_tolerance_unit_

String fragment_mass_tolerance_unit_

protected

## ◆ modifications_fixed_

StringList modifications_fixed_

protected

## ◆ modifications_max_variable_mods_per_peptide_

Size modifications_max_variable_mods_per_peptide_

protected

## ◆ modifications_variable_

StringList modifications_variable_

protected

## ◆ peptide_max_size_

Size peptide_max_size_

protected

## ◆ peptide_min_size_

Size peptide_min_size_

protected

## ◆ peptide_missed_cleavages_

Size peptide_missed_cleavages_

protected

## ◆ peptide_motif_

String peptide_motif_

protected

## ◆ precursor_isotopes_

IntList precursor_isotopes_

protected

## ◆ precursor_mass_tolerance_

double precursor_mass_tolerance_

protected

## ◆ precursor_mass_tolerance_unit_

String precursor_mass_tolerance_unit_

protected

## ◆ precursor_max_charge_

Size precursor_max_charge_

protected

## ◆ precursor_min_charge_

Size precursor_min_charge_

protected

## ◆ report_top_hits_

Size report_top_hits_

protected