This class implements the database preprocessing needing for precursor ion selection. More...
#include <OpenMS/ANALYSIS/TARGETED/PrecursorIonSelectionPreprocessing.h>
 
  
 | Public Member Functions | |
| PrecursorIonSelectionPreprocessing () | |
| PrecursorIonSelectionPreprocessing (const PrecursorIonSelectionPreprocessing &source) | |
| ~PrecursorIonSelectionPreprocessing () | |
| PrecursorIonSelectionPreprocessing & | operator= (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 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... | |
| 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< DoubleReal > | 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 < DoubleReal > > | prot_masses_ | 
| stores masses of tryptic peptides for proteins, key is the accession number  More... | |
| std::vector< DoubleReal > | 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 < 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< 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... | |
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 | min: 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 | min: 1 | Minimal RT in the experiment (in seconds) | 
| rt_settings:max_rt | float | 3840 | Maximal RT in the experiment (in seconds) | |
| rt_settings:rt_step_size | float | 30 | Time between two consecutive spectra (in seconds) | |
| rt_settings:gauss_mean | float | -1 | mean of the gauss curve | |
| rt_settings:gauss_sigma | float | 3 | std of the gauss curve | 
| PrecursorIonSelectionPreprocessing | ( | const PrecursorIonSelectionPreprocessing & | source | ) | 
| void dbPreprocessing | ( | String | db_path, | 
| bool | save = true | ||
| ) | 
Calculates tryptric peptide masses of a given database and stores masses and peptide sequences.
| db_path | Path to database file (fasta) | 
| save | Flag if preprocessing should be stored. | 
| Exception::FileNotFound | if file with preprocessing or db can't be found | 
| Exception::UnableToCreateFile | if 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.
| db_path | Path to database file (fasta) | 
| rt_model_path | |
| dt_model_path | |
| save | Flag if preprocessing should be stored. | 
| Exception::FileNotFound | if file with preprocessing or db can't be found | 
| Exception::UnableToCreateFile | if preprocessing file can't be written | 
| 
 | protected | 
preprocess fasta identifier
| 
 | inline | 
| 
 | inline | 
| 
 | inline | 
| const std::vector<DoubleReal>& getMasses | ( | String | acc | ) | 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 | ||
| ) | 
| 
 | protected | 
| 
 | protected | 
| DoubleReal getWeight | ( | DoubleReal | mass | ) | 
get the weighted frequency of a mass
| 
 | protected | 
loads the preprocessed db
| void loadPreprocessing | ( | ) | 
Loads tryptric peptide masses of a given database.
| 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 | 
| PrecursorIonSelectionPreprocessing& operator= | ( | const PrecursorIonSelectionPreprocessing & | source | ) | 
| void setFixedModifications | ( | StringList & | modifications | ) | 
| void setGaussianParameters | ( | DoubleReal | mu, | 
| DoubleReal | sigma | ||
| ) | 
| 
 | protectedvirtual | 
update members method from DefaultParamHandler to update the members
Reimplemented from DefaultParamHandler.
| 
 | protected | 
the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm)
| 
 | protected | 
counter for the bins
| 
 | protected | 
maximal relative frequency of a mass
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
all tryptic masses of the distinct peptides in the database
| 
 | protected | 
| 
 | protected | 
stores masses of tryptic peptides for proteins, key is the accession number
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
the sequences of the tryptic peptides
| 
 | protected | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |