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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:
DefaultParamHandler

Public Member Functions

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

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)
 preprocess fasta identifier More...
 
Int getScanNumber_ (DoubleReal rt)
 
DoubleReal getRTProbability_ (DoubleReal min_obs_rt, DoubleReal max_obs_rt, DoubleReal pred_rt)
 
void updateMembers_ ()
 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< DoubleRealmasses_
 all tryptic masses of the distinct peptides in the database More...
 
std::set< AASequencesequences_
 the sequences of the tryptic peptides More...
 
std::map< String, std::vector
< DoubleReal > > 
prot_masses_
 stores masses of tryptic peptides for proteins, key is the accession number More...
 
std::vector< DoubleRealbin_masses_
 the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm) More...
 
std::vector< UIntcounter_
 counter for the bins More...
 
UInt f_max_
 maximal relative frequency of a mass More...
 
bool fixed_mods_
 
std::map< String, std::vector
< DoubleReal > > 
rt_prot_map_
 
std::map< String, std::vector
< DoubleReal > > 
pt_prot_map_
 
std::map< String, std::vector
< String > > 
prot_peptide_seq_map_
 
std::map< char, std::vector
< String > > 
fixed_modifications_
 
DoubleReal sigma_
 
DoubleReal 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< 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...
 

Detailed Description

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

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
precursor_mass_tolerance float10 min: 0Precursor mass tolerance which is used to query the peptide database for peptides
precursor_mass_tolerance_unit stringppm ppm, DaPrecursor 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 int100000 min: 1Number of peptides for that the pt and rt are parallely predicted.
missed_cleavages int1 min: 0Number 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 stringfalse  Flag if peptide sequences should be stored.
rt_settings:min_rt float960 min: 1Minimal RT in the experiment (in seconds)
rt_settings:max_rt float3840  Maximal RT in the experiment (in seconds)
rt_settings:rt_step_size float30  Time between two consecutive spectra (in seconds)
rt_settings:gauss_mean float-1  mean of the gauss curve
rt_settings:gauss_sigma float3  std of the gauss curve

Note:

Constructor & Destructor Documentation

Member Function Documentation

void dbPreprocessing ( String  db_path,
bool  save = true 
)

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

Parameters
db_pathPath to database file (fasta)
saveFlag if preprocessing should be stored.
Exceptions
Exception::FileNotFoundif file with preprocessing or db can't be found
Exception::UnableToCreateFileif preprocessing file can't be written
void dbPreprocessing ( String  db_path,
String  rt_model_path,
String  dt_model_path,
bool  save = true 
)

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

Parameters
db_pathPath to database file (fasta)
rt_model_path
dt_model_path
saveFlag if preprocessing should be stored.
Exceptions
Exception::FileNotFoundif file with preprocessing or db can't be found
Exception::UnableToCreateFileif preprocessing file can't be written
void filterTaxonomyIdentifier_ ( FASTAFile::FASTAEntry entry)
protected

preprocess fasta identifier

const std::map<char, std::vector<String> >& getFixedModifications ( )
inline
DoubleReal getGaussMu ( )
inline
DoubleReal getGaussSigma ( )
inline
const std::vector<DoubleReal>& getMasses ( String  acc) const
const std::map<String, std::vector<String> >& getProteinPeptideSequenceMap ( ) const
const std::map<String, std::vector<DoubleReal> >& getProteinPTMap ( ) const
const std::map<String, std::vector<DoubleReal> >& getProteinRTMap ( ) const
const std::map<String, std::vector<DoubleReal> >& getProtMasses ( ) const
DoubleReal getPT ( String  prot_id,
Size  peptide_index 
)
DoubleReal getRT ( String  prot_id,
Size  peptide_index 
)
DoubleReal getRTProbability ( String  prot_id,
Size  peptide_index,
Feature feature 
)
DoubleReal getRTProbability ( DoubleReal  pred_rt,
Feature feature 
)
DoubleReal getRTProbability_ ( DoubleReal  min_obs_rt,
DoubleReal  max_obs_rt,
DoubleReal  pred_rt 
)
protected
Int getScanNumber_ ( DoubleReal  rt)
protected
DoubleReal getWeight ( DoubleReal  mass)

get the weighted frequency of a mass

void loadPreprocessedDB_ ( String  path)
protected

loads the preprocessed db

void loadPreprocessing ( )

Loads tryptric peptide masses of a given database.

Exceptions
Exception::FileNotFoundif file with preprocessing can't be found
Exception::InvalidParameterif precursor_mass_tolerance_unit is ppm and file containing bin borders can't be found
void savePreprocessedDB_ ( String  db_path,
String  path 
)
protected

saves the preprocessed db

void savePreprocessedDBWithRT_ ( String  db_path,
String  path 
)
protected
void setFixedModifications ( StringList modifications)
void setGaussianParameters ( DoubleReal  mu,
DoubleReal  sigma 
)
void updateMembers_ ( )
protectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Member Data Documentation

std::vector<DoubleReal> bin_masses_
protected

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

std::vector<UInt> counter_
protected

counter for the bins

UInt f_max_
protected

maximal relative frequency of a mass

std::map<char, std::vector<String> > fixed_modifications_
protected
bool fixed_mods_
protected
std::vector<DoubleReal> masses_
protected

all tryptic masses of the distinct peptides in the database

DoubleReal mu_
protected
std::map<String, std::vector<DoubleReal> > prot_masses_
protected

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

std::map<String, std::vector<String> > prot_peptide_seq_map_
protected
std::map<String, std::vector<DoubleReal> > pt_prot_map_
protected
std::map<String, std::vector<DoubleReal> > rt_prot_map_
protected
std::set<AASequence> sequences_
protected

the sequences of the tryptic peptides

DoubleReal sigma_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5