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 |
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preprocess fasta identifier
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| 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 | ||
| ) |
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| DoubleReal getWeight | ( | DoubleReal | mass | ) |
get the weighted frequency of a mass
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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 | ||
| ) |
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update members method from DefaultParamHandler to update the members
Reimplemented from DefaultParamHandler.
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the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm)
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counter for the bins
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maximal relative frequency of a mass
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all tryptic masses of the distinct peptides in the database
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stores masses of tryptic peptides for proteins, key is the accession number
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the sequences of the tryptic peptides
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |