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SuffixArrayTrypticSeqan Class Reference

#include <OpenMS/DATASTRUCTURES/SuffixArrayTrypticSeqan.h>

Inheritance diagram for SuffixArrayTrypticSeqan:

SuffixArraySeqan SuffixArray

List of all members.


Detailed Description

Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum.

This class uses SEQAN suffix array. It can just be used for finding peptide Candidates for a given MS Spectrum within a certain mass tolerance. The suffix array can be saved to disc for reused so it has to be build just once.

Public Member Functions

 SuffixArrayTrypticSeqan (const String &st, const String &sa_file_name) throw (Exception::InvalidValue,Exception::FileNotFound)
bool isDigestingEnd (const char aa1, const char aa2) const
 returns if an enzyme will cut after first character


Constructor & Destructor Documentation

SuffixArrayTrypticSeqan ( const String st,
const String sa_file_name 
) throw (Exception::InvalidValue,Exception::FileNotFound)


Member Function Documentation

bool isDigestingEnd ( const char  aa1,
const char  aa2 
) const [virtual]

returns if an enzyme will cut after first character

Parameters:
aa1 const char as first aminoacid
aa2 const char as second aminoacid
Returns:
bool descibing if it is a digesting site

Reimplemented from SuffixArraySeqan.


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