| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
PrecursorIonSelectionPreprocessing Class Reference

This class implements the database preprocessing needing for precursor ion selection. More...

`#include <OpenMS/ANALYSIS/TARGETED/PrecursorIonSelectionPreprocessing.h>`

Inheritance diagram for PrecursorIonSelectionPreprocessing:

## Public Member Functions

| PrecursorIonSelectionPreprocessing ()
| PrecursorIonSelectionPreprocessing (const PrecursorIonSelectionPreprocessing &source)
| ~PrecursorIonSelectionPreprocessing () override
PrecursorIonSelectionPreprocessing & | operator= (const PrecursorIonSelectionPreprocessing &source)
const std::map< String, std::vector< double > > & | getProtMasses () const
const std::vector< double > & | getMasses (String acc) const
const std::map< String, std::vector< double > > & | getProteinRTMap () const
const std::map< String, std::vector< double > > & | getProteinPTMap () const
const std::map< String, std::vector< String > > & | getProteinPeptideSequenceMap () const
void | dbPreprocessing (String db_path, bool save=true)
| Calculates tryptic peptide masses of a given database and stores masses and peptide sequences. More...
void | dbPreprocessing (String db_path, String rt_model_path, String dt_model_path, bool save=true)
| Calculates tryptic peptide masses of a given database and stores masses and peptide sequences. More...
void | loadPreprocessing ()
| Loads tryptic peptide masses of a given database. More...
double | getWeight (double mass)
| get the weighted frequency of a mass More...
double | getRT (String prot_id, Size peptide_index)
double | getPT (String prot_id, Size peptide_index)
void | setFixedModifications (StringList &modifications)
const std::map< char, std::vector< String > > & | getFixedModifications ()
void | setGaussianParameters (double mu, double sigma)
double | getGaussMu ()
double | getGaussSigma ()
double | getRTProbability (String prot_id, Size peptide_index, Feature &feature)
double | getRTProbability (double pred_rt, Feature &feature)
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...

## Protected Member Functions

void | savePreprocessedDB_ (String db_path, String path)
| saves the preprocessed db More...
void | savePreprocessedDBWithRT_ (String db_path, String path)
void | loadPreprocessedDB_ (String path)
| loads the preprocessed db More...
void | filterTaxonomyIdentifier_ (FASTAFile::FASTAEntry &entry)
| pre-process fasta identifier More...
Int | getScanNumber_ (double rt)
double | getRTProbability_ (double min_obs_rt, double max_obs_rt, double pred_rt)
void | updateMembers_ () override
| update members method from DefaultParamHandler to update the members More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

std::vector< double > | masses_
| all tryptic masses of the distinct peptides in the database More...
std::set< AASequence > | sequences_
| the sequences of the tryptic peptides More...
std::map< String, std::vector< double > > | prot_masses_
| stores masses of tryptic peptides for proteins, key is the accession number More...
std::vector< double > | bin_masses_
| the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm) More...
std::vector< UInt > | counter_
| counter for the bins More...
UInt | f_max_
| maximal relative frequency of a mass More...
bool | fixed_mods_
std::map< String, std::vector< double > > | rt_prot_map_
std::map< String, std::vector< double > > | pt_prot_map_
std::map< String, std::vector< String > > | prot_peptide_seq_map_
std::map< char, std::vector< String > > | fixed_modifications_
double | sigma_
double | mu_
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...

## Detailed Description

This class implements the database preprocessing needing for precursor ion selection.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
precursor_mass_tolerance | float | 10.0 | min: 0.0 | Precursor mass tolerance which is used to query the peptide database for peptides
precursor_mass_tolerance_unit | string | ppm | ppm, Da | Precursor mass tolerance unit.
preprocessed_db_path | string |  |  | Path where the preprocessed database should be stored
preprocessed_db_pred_rt_path | string |  |  | Path where the predicted rts of the preprocessed database should be stored
preprocessed_db_pred_dt_path | string |  |  | Path where the predicted rts of the preprocessed database should be stored
max_peptides_per_run | int | 100000 | min: 1 | Number of peptides for that the pt and rt are parallely predicted.
missed_cleavages | int | 1 | min: 0 | Number of allowed missed cleavages.
taxonomy | string |  |  | Taxonomy
tmp_dir | string |  |  | Absolute path to tmp data directory used to store files needed for rt and dt prediction.
store_peptide_sequences | string | false |  | Flag if peptide sequences should be stored.
rt_settings:min_rt | float | 960.0 | min: 1.0 | Minimal RT in the experiment (in seconds)
rt_settings:max_rt | float | 3840.0 |  | Maximal RT in the experiment (in seconds)
rt_settings:rt_step_size | float | 30.0 |  | Time between two consecutive spectra (in seconds)
rt_settings:gauss_mean | float | -1.0 |  | mean of the gauss curve
rt_settings:gauss_sigma | float | 3.0 |  | std of the gauss curve

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Constructor & Destructor Documentation

## ◆ PrecursorIonSelectionPreprocessing() [1/2]

PrecursorIonSelectionPreprocessing | ( |  | ) |

## ◆ PrecursorIonSelectionPreprocessing() [2/2]

PrecursorIonSelectionPreprocessing | ( | const PrecursorIonSelectionPreprocessing & | source | ) |

## ◆ ~PrecursorIonSelectionPreprocessing()

~PrecursorIonSelectionPreprocessing | ( |  | ) |

override

## Member Function Documentation

## ◆ dbPreprocessing() [1/2]

void dbPreprocessing | ( | String | db_path,
|  | bool | save = `true`
| ) |  |

Calculates tryptic peptide masses of a given database and stores masses and peptide sequences.

Parameters

  db_path | Path to database file (fasta)
  save | Flag if preprocessing should be stored.

Exceptions

  Exception::FileNotFound | if file with preprocessing or db can't be found
  Exception::UnableToCreateFile | if preprocessing file can't be written

## ◆ dbPreprocessing() [2/2]

void dbPreprocessing | ( | String | db_path,
|  | String | rt_model_path,
|  | String | dt_model_path,
|  | bool | save = `true`
| ) |  |

Calculates tryptic peptide masses of a given database and stores masses and peptide sequences.

Parameters

  db_path | Path to database file (fasta)
  rt_model_path |
  dt_model_path |
  save | Flag if preprocessing should be stored.

Exceptions

  Exception::FileNotFound | if file with preprocessing or db can't be found
  Exception::UnableToCreateFile | if preprocessing file can't be written

## ◆ filterTaxonomyIdentifier_()

void filterTaxonomyIdentifier_ | ( | FASTAFile::FASTAEntry & | entry | ) |

protected

pre-process fasta identifier

## ◆ getFixedModifications()

const std::map<char, std::vector<String> >& getFixedModifications | ( |  | ) |

inline

## ◆ getGaussMu()

double getGaussMu | ( |  | ) |

inline

## ◆ getGaussSigma()

double getGaussSigma | ( |  | ) |

inline

## ◆ getMasses()

const std::vector<double>& getMasses | ( | String | acc | ) | const

## ◆ getProteinPeptideSequenceMap()

const std::map<String, std::vector<String> >& getProteinPeptideSequenceMap | ( |  | ) | const

## ◆ getProteinPTMap()

const std::map<String, std::vector<double> >& getProteinPTMap | ( |  | ) | const

## ◆ getProteinRTMap()

const std::map<String, std::vector<double> >& getProteinRTMap | ( |  | ) | const

## ◆ getProtMasses()

const std::map<String, std::vector<double> >& getProtMasses | ( |  | ) | const

## ◆ getPT()

double getPT | ( | String | prot_id,
|  | Size | peptide_index
| ) |  |

## ◆ getRT()

double getRT | ( | String | prot_id,
|  | Size | peptide_index
| ) |  |

## ◆ getRTProbability() [1/2]

double getRTProbability | ( | String | prot_id,
|  | Size | peptide_index,
|  | Feature & | feature
| ) |  |

## ◆ getRTProbability() [2/2]

double getRTProbability | ( | double | pred_rt,
|  | Feature & | feature
| ) |  |

## ◆ getRTProbability_()

double getRTProbability_ | ( | double | min_obs_rt,
|  | double | max_obs_rt,
|  | double | pred_rt
| ) |  |

protected

## ◆ getScanNumber_()

Int getScanNumber_ | ( | double | rt | ) |

protected

## ◆ getWeight()

double getWeight | ( | double | mass | ) |

get the weighted frequency of a mass

## ◆ loadPreprocessedDB_()

void loadPreprocessedDB_ | ( | String | path | ) |

protected

loads the preprocessed db

## ◆ loadPreprocessing()

void loadPreprocessing | ( |  | ) |

Loads tryptic peptide masses of a given database.

Exceptions

  Exception::FileNotFound | if file with preprocessing can't be found
  Exception::InvalidParameter | if precursor_mass_tolerance_unit is ppm and file containing bin borders can't be found

## ◆ operator=()

PrecursorIonSelectionPreprocessing& operator= | ( | const PrecursorIonSelectionPreprocessing & | source | ) |

## ◆ savePreprocessedDB_()

void savePreprocessedDB_ | ( | String | db_path,
|  | String | path
| ) |  |

protected

saves the preprocessed db

## ◆ savePreprocessedDBWithRT_()

void savePreprocessedDBWithRT_ | ( | String | db_path,
|  | String | path
| ) |  |

protected

## ◆ setFixedModifications()

void setFixedModifications | ( | StringList & | modifications | ) |

## ◆ setGaussianParameters()

void setGaussianParameters | ( | double | mu,
|  | double | sigma
| ) |  |

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ bin_masses_

std::vector<double> bin_masses_

protected

the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm)

## ◆ counter_

std::vector<UInt> counter_

protected

counter for the bins

## ◆ f_max_

UInt f_max_

protected

maximal relative frequency of a mass

## ◆ fixed_modifications_

std::map<char, std::vector<String> > fixed_modifications_

protected

## ◆ fixed_mods_

bool fixed_mods_

protected

## ◆ masses_

std::vector<double> masses_

protected

all tryptic masses of the distinct peptides in the database

## ◆ mu_

double mu_

protected

## ◆ prot_masses_

std::map<String, std::vector<double> > prot_masses_

protected

stores masses of tryptic peptides for proteins, key is the accession number

## ◆ prot_peptide_seq_map_

std::map<String, std::vector<String> > prot_peptide_seq_map_

protected

## ◆ pt_prot_map_

std::map<String, std::vector<double> > pt_prot_map_

protected

## ◆ rt_prot_map_

std::map<String, std::vector<double> > rt_prot_map_

protected

## ◆ sequences_

std::set<AASequence> sequences_

protected

the sequences of the tryptic peptides

## ◆ sigma_

double sigma_

protected