Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Types | Public Member Functions | Protected Member Functions | Protected Attributes

SuffixArrayPeptideFinder Class Reference

wrapper for easy use of sufArray More...

#include <OpenMS/DATASTRUCTURES/SuffixArrayPeptideFinder.h>

Inheritance diagram for SuffixArrayPeptideFinder:
WeightWrapper

List of all members.

Public Types

typedef std::pair< String, String > FASTAEntry

Public Member Functions

 SuffixArrayPeptideFinder (const String &filename, const String &method, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO)
 constructor
 SuffixArrayPeptideFinder (const SuffixArrayPeptideFinder &source)
 copy constructor
virtual ~SuffixArrayPeptideFinder ()
 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
void getCandidates (std::vector< std::vector< std::pair< FASTAEntry, String > > > &candidates, const String &DTA_file)
 finds all candidate for given DTA file
void setTolerance (const DoubleReal t)
 allowed tolerance for mass match
DoubleReal getTolerance () const
 allowed tolerance for mass match
void setNumberOfModifications (Size number_of_mods) const
 setter for number of modifications
Size getNumberOfModifications () const
 getter for number of modifications
void setTags (const std::vector< String > &tags)
 setter for tags
const std::vector< 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)
 set modification output method (valid are: "mass", "stringUnchecked", "stringChecked")
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

Detailed Description

wrapper for easy use of sufArray

Member Typedef Documentation

typedef std::pair<String, String> FASTAEntry

Constructor & Destructor Documentation

SuffixArrayPeptideFinder ( const String &  filename,
const String &  method,
const WeightWrapper::WEIGHTMODE  weight_mode = WeightWrapper::MONO 
)

constructor

Parameters:
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
Exceptions:
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 ~SuffixArrayPeptideFinder (  )  [virtual]

destructor

Member Function Documentation

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

Parameters:
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()
See also:
sufArray.h
void getCandidates ( std::vector< std::vector< std::pair< FASTAEntry, String > > > &  candidates,
const String &  DTA_file 
)

finds all candidate for given DTA file

Parameters:
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()
Exceptions:
FileNotFound if DTA file does not exists
ParseError is thrown if the dta file could not be parsed
See also:
sufArray.h
String getModificationOutputMethod (  ) 

getter for modification output method

Returns:
String
Size getNumberOfModifications (  )  const

getter for number of modifications

Returns:
number of modifications
const std::vector<String>& getTags (  ) 

getter for tags

Returns:
const reference to vector of strings
DoubleReal getTolerance (  )  const

allowed tolerance for mass match

Returns:
Tolerance in u
bool getUseTags (  ) 

getter for use_tags

Returns:
bool indicating whether tags are used or not
void setModificationOutputMethod ( const String &  s  ) 

set modification output method (valid are: "mass", "stringUnchecked", "stringChecked")

Parameters:
s describing how modifications sould be given back
Exceptions:
InvalidValue is thrown if method s is not known
void setNumberOfModifications ( Size  number_of_mods  )  const

setter for number of modifications

Parameters:
number_of_mods 
void setTags ( const std::vector< String > &  tags  ) 

setter for tags

Parameters:
tags reference to vector of strings with tags
Note:
sets use_tags = true
void setTolerance ( const DoubleReal  t  ) 

allowed tolerance for mass match

Parameters:
t Tolerance in u
void setUseTags ( bool  use_tags  ) 

setter for use_tags

Parameters:
use_tags indicating whether tags should be used or not
String vToString_ ( std::vector< String >  v  )  [protected]

Member Data Documentation

BigString big_string_ [protected]

bigString object holding all peptides of fasta file

String modification_output_method_ [protected]

output method for modifications

SuffixArray* sa_ [protected]

pointer to suffixarray

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1