Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum. More...
#include <OpenMS/DATASTRUCTURES/SuffixArrayTrypticSeqan.h>
Inheritance diagram for SuffixArrayTrypticSeqan:
Public Member Functions | |
| SuffixArrayTrypticSeqan (const String &st, const String &filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO) | |
| constructor for tryptic seqan array with a specially optimized implementation | |
| bool | isDigestingEnd (const char aa1, const char aa2) const |
| returns if an enzyme will cut after first character | |
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.
Constructor & Destructor Documentation
| SuffixArrayTrypticSeqan | ( | const String & | st, | |
| const String & | filename, | |||
| const WeightWrapper::WEIGHTMODE | weight_mode = WeightWrapper::MONO | |||
| ) |
constructor for tryptic seqan array with a specially optimized implementation
- Parameters:
-
st the suffix array string, which is used to build the suffix array filename filename of fasta file weight_mode if not monoistopic weight should be used, this parameters can be set to AVERAGE
- Exceptions:
-
InvalidValue is thrown if string st if invalid FileNotFound is thrown if given file is not found
Member Function Documentation
| bool isDigestingEnd | ( | const char | aa1, | |
| const char | aa2 | |||
| ) | const |
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.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1 |