wrapper for easy use of sufArray More...
#include <OpenMS/DATASTRUCTURES/SuffixArrayPeptideFinder.h>
Public Types | |
| typedef std::pair< String, String > | FASTAEntry |
Public Types inherited from WeightWrapper | |
| enum | WEIGHTMODE { AVERAGE = 0, MONO, SIZE_OF_WEIGHTMODE } |
Public Member Functions | |
| SuffixArrayPeptideFinder (const String &filename, const String &method, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO) | |
| constructor More... | |
| SuffixArrayPeptideFinder (const SuffixArrayPeptideFinder &source) | |
| copy constructor More... | |
| virtual | ~SuffixArrayPeptideFinder () |
| destructor More... | |
| void | getCandidates (std::vector< std::vector< std::pair< FASTAEntry, String > > > &candidates, const std::vector< DoubleReal > &spec) |
| finds all candidates for given spectrum in the suffix array More... | |
| void | getCandidates (std::vector< std::vector< std::pair< FASTAEntry, String > > > &candidates, const String &DTA_file) |
| finds all candidate for given DTA file More... | |
| void | setTolerance (const DoubleReal t) |
| allowed tolerance for mass match More... | |
| DoubleReal | getTolerance () const |
| allowed tolerance for mass match More... | |
| void | setNumberOfModifications (Size number_of_mods) const |
| setter for number of modifications More... | |
| Size | getNumberOfModifications () const |
| getter for number of modifications More... | |
| void | setTags (const std::vector< String > &tags) |
| setter for tags More... | |
| const std::vector< String > & | getTags () |
| getter for tags More... | |
| void | setUseTags (bool use_tags) |
| setter for use_tags More... | |
| bool | getUseTags () |
| getter for use_tags More... | |
| void | setModificationOutputMethod (const String &s) |
| set modification output method (valid are: "mass", "stringUnchecked", "stringChecked") More... | |
| String | getModificationOutputMethod () |
| getter for modification output method More... | |
Public Member Functions inherited from WeightWrapper | |
| WeightWrapper () | |
| constructor More... | |
| WeightWrapper (const WEIGHTMODE weight_mode) | |
| constructor More... | |
| virtual | ~WeightWrapper () |
| destructor More... | |
| WeightWrapper (const WeightWrapper &source) | |
| copy constructor More... | |
| void | setWeightMode (const WEIGHTMODE mode) |
| Sets the weight mode (MONO or AVERAGE) More... | |
| WEIGHTMODE | getWeightMode () const |
| Gets the weight mode (MONO or AVERAGE) More... | |
| DoubleReal | getWeight (const AASequence &aa) const |
| returns the weight of either mono or average value More... | |
| DoubleReal | getWeight (const EmpiricalFormula &ef) const |
| returns the weight of either mono or average value More... | |
| DoubleReal | getWeight (const Residue &r, Residue::ResidueType res_type=Residue::Full) const |
| returns the weight of either mono or average value More... | |
Protected Member Functions | |
| String | vToString_ (std::vector< String > v) |
Protected Attributes | |
| BigString | big_string_ |
| bigString object holding all peptides of fasta file More... | |
| SuffixArray * | sa_ |
| pointer to suffixarray More... | |
| String | modification_output_method_ |
| output method for modifications More... | |
wrapper for easy use of sufArray
| typedef std::pair<String, String> FASTAEntry |
| SuffixArrayPeptideFinder | ( | const String & | filename, |
| const String & | method, | ||
| const WeightWrapper::WEIGHTMODE | weight_mode = WeightWrapper::MONO |
||
| ) |
constructor
| filename | FASTA File name |
| method | Name of the method used (trypticCompressed, seqan, trypticSeqan) |
| weight_mode | if not monoistopic weight should be used, this parameters can be set to AVERAGE |
| FileNotFound | is thrown if the filename is not found |
| ParseError | is thrown if a error in parsing of the fasta file occurs |
| InvalidValue | is thrown if an unknown method is supplied |
| SuffixArrayPeptideFinder | ( | const SuffixArrayPeptideFinder & | source | ) |
copy constructor
|
virtual |
destructor
| void getCandidates | ( | std::vector< std::vector< std::pair< FASTAEntry, String > > > & | candidates, |
| const std::vector< DoubleReal > & | spec | ||
| ) |
finds all candidates for given spectrum in the suffix array
| spec | vector holding the mass values to query |
| candidates | Output holding the candidates for input masses (one vector per mass) FASTAEntry contains the FASTA header and the peptide sequence The String contains the modification (if any) in the format specified by getModificationOutputMethod() |
| void getCandidates | ( | std::vector< std::vector< std::pair< FASTAEntry, String > > > & | candidates, |
| const String & | DTA_file | ||
| ) |
finds all candidate for given DTA file
| DTA_file | DTA file location |
| candidates | Output parameters which holds the candidates suitable for the mass given in the dta file FASTAEntry contains the FASTA header and the peptide sequence The String contains the modification (if any) in the format specified by getModificationOutputMethod() |
| FileNotFound | if DTA file does not exists |
| ParseError | is thrown if the dta file could not be parsed |
| Size getNumberOfModifications | ( | ) | const |
getter for number of modifications
| const std::vector<String>& getTags | ( | ) |
getter for tags
| DoubleReal getTolerance | ( | ) | const |
allowed tolerance for mass match
| bool getUseTags | ( | ) |
getter for use_tags
| void setModificationOutputMethod | ( | const String & | s | ) |
set modification output method (valid are: "mass", "stringUnchecked", "stringChecked")
| s | describing how modifications sould be given back |
| InvalidValue | is thrown if method s is not known |
| void setNumberOfModifications | ( | Size | number_of_mods | ) | const |
setter for number of modifications
| number_of_mods |
| void setTags | ( | const std::vector< String > & | tags | ) |
setter for tags
| tags | reference to vector of strings with tags |
| void setTolerance | ( | const DoubleReal | t | ) |
allowed tolerance for mass match
| t | Tolerance in u |
| void setUseTags | ( | bool | use_tags | ) |
setter for use_tags
| use_tags | indicating whether tags should be used or not |
|
protected |
bigString object holding all peptides of fasta file
|
protected |
output method for modifications
|
protected |
pointer to suffixarray
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:29 using doxygen 1.8.5 |