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SuffixArrayPeptideFinder Class Reference

#include <OpenMS/DATASTRUCTURES/SuffixArrayPeptideFinder.h>

List of all members.


Detailed Description

wrapper for easy use of sufArray

Public Types

typedef std::pair< String, StringFASTAEntry

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
SuffixArraysa_
 pointer to suffixarray
String modification_output_method_
 output method for modifications

Member Typedef Documentation

typedef std::pair<String, String> FASTAEntry


Constructor & Destructor Documentation

SuffixArrayPeptideFinder ( const String fFile,
const String method 
) throw (Exception::FileNotFound,Exception::ParseError,Exception::InvalidValue)

constructor

Parameters:
fFile const string for location of FASTA File

SuffixArrayPeptideFinder ( const SuffixArrayPeptideFinder source  ) 

copy constructor

virtual ~SuffixArrayPeptideFinder (  )  [virtual]

destructor


Member Function Documentation

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

Parameters:
spec const reference to float vector describing the MS spectrum
Returns:
for every mass a entry with all Candidates as vector of FASTAEntrys
See also:
sufArray.h

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

Parameters:
DTAFile DTA file location
Returns:
for every mass a entry with all Candidates as vector of FASTAEntrys
Exceptions:
Exception::FileNotFound if DTA file does not exists
See also:
sufArray.h

void setTolerance ( const float  t  ) 

setter for tolerance

Parameters:
t const float tolerance

float getTolerance (  )  const

getter for tolerance

Returns:
float with tolerance

void setNumberOfModifications ( UInt  number_of_mods  )  const

setter for number of modifications

Parameters:
number_of_mods 

UInt getNumberOfModifications (  )  const

getter for number of modifications

Returns:
number of modifications

void setTags ( const std::vector< OpenMS::String > &  tags  )  throw (OpenMS::Exception::InvalidValue)

setter for tags

Parameters:
tags reference to vector of strings with tags
Note:
sets use_tags = true

const std::vector<OpenMS::String>& getTags (  ) 

getter for tags

Returns:
const reference to vector of strings

void setUseTags ( bool  use_tags  ) 

setter for use_tags

Parameters:
use_tags indicating whether tags should be used or not

bool getUseTags (  ) 

getter for use_tags

Returns:
bool indicating whether tags are used or not

void setModificationOutputMethod ( const String s  )  throw (OpenMS::Exception::InvalidValue)

setter for modification output method

Parameters:
s describing how modifications sould be given back

String getModificationOutputMethod (  ) 

getter for modification output method

Returns:
String

String vToString_ ( std::vector< String v  )  [protected]


Member Data Documentation

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


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1