#include <OpenMS/DATASTRUCTURES/SuffixArrayPeptideFinder.h>
Public Types | |
typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
SuffixArrayPeptideFinder (const String &fFile, const String &method) throw (Exception::FileNotFound,Exception::ParseError,Exception::InvalidValue) | |
constructor | |
SuffixArrayPeptideFinder (const SuffixArrayPeptideFinder &source) | |
copy constructor | |
virtual | ~SuffixArrayPeptideFinder () |
destructor | |
void | getCandidates (std::vector< std::vector< std::pair< FASTAEntry, String > > > &candidates, const std::vector< double > &spec) |
finds all candidate for given spectrum in the suffix array | |
void | getCandidates (std::vector< std::vector< std::pair< FASTAEntry, String > > > &candidates, const String &DTA_file) throw (Exception::FileNotFound,Exception::ParseError) |
finds all candidate for given DTA file | |
void | setTolerance (const float t) |
setter for tolerance | |
float | getTolerance () const |
getter for tolerance | |
void | setNumberOfModifications (UInt number_of_mods) const |
setter for number of modifications | |
UInt | getNumberOfModifications () const |
getter for number of modifications | |
void | setTags (const std::vector< OpenMS::String > &tags) throw (OpenMS::Exception::InvalidValue) |
setter for tags | |
const std::vector < OpenMS::String > & | getTags () |
getter for tags | |
void | setUseTags (bool use_tags) |
setter for use_tags | |
bool | getUseTags () |
getter for use_tags | |
void | setModificationOutputMethod (const String &s) throw (OpenMS::Exception::InvalidValue) |
setter for modification output method | |
String | getModificationOutputMethod () |
getter for modification output method | |
Protected Member Functions | |
String | vToString_ (std::vector< String > v) |
Protected Attributes | |
BigString | big_string_ |
bigString object holding all peptides of fasta file | |
SuffixArray * | sa_ |
pointer to suffixarray | |
String | modification_output_method_ |
output method for modifications |
typedef std::pair<String, String> FASTAEntry |
SuffixArrayPeptideFinder | ( | const String & | fFile, | |
const String & | method | |||
) | throw (Exception::FileNotFound,Exception::ParseError,Exception::InvalidValue) |
SuffixArrayPeptideFinder | ( | const SuffixArrayPeptideFinder & | source | ) |
copy constructor
virtual ~SuffixArrayPeptideFinder | ( | ) | [virtual] |
destructor
void getCandidates | ( | std::vector< std::vector< std::pair< FASTAEntry, String > > > & | candidates, | |
const std::vector< double > & | spec | |||
) |
finds all candidate for given spectrum in the suffix array
spec | const reference to float vector describing the MS spectrum |
void getCandidates | ( | std::vector< std::vector< std::pair< FASTAEntry, String > > > & | candidates, | |
const String & | DTA_file | |||
) | throw (Exception::FileNotFound,Exception::ParseError) |
finds all candidate for given DTA file
DTAFile | DTA file location |
Exception::FileNotFound | if DTA file does not exists |
void setTolerance | ( | const float | t | ) |
setter for tolerance
t | const float tolerance |
float getTolerance | ( | ) | const |
getter for tolerance
void setNumberOfModifications | ( | UInt | number_of_mods | ) | const |
setter for number of modifications
number_of_mods |
UInt getNumberOfModifications | ( | ) | const |
getter for number of modifications
void setTags | ( | const std::vector< OpenMS::String > & | tags | ) | throw (OpenMS::Exception::InvalidValue) |
setter for tags
tags | reference to vector of strings with tags |
const std::vector<OpenMS::String>& getTags | ( | ) |
getter for tags
void setUseTags | ( | bool | use_tags | ) |
setter for use_tags
use_tags | indicating whether tags should be used or not |
bool getUseTags | ( | ) |
getter for use_tags
void setModificationOutputMethod | ( | const String & | s | ) | throw (OpenMS::Exception::InvalidValue) |
setter for modification output method
s | describing how modifications sould be given back |
BigString big_string_ [protected] |
bigString object holding all peptides of fasta file
SuffixArray* sa_ [protected] |
pointer to suffixarray
String modification_output_method_ [protected] |
output method for modifications
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |