Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum.  
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|  | SuffixArrayTrypticSeqan (const String &st, const String &filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO) | 
|  | constructor for tryptic seqan array with a specially optimized implementation  More... 
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| bool | isDigestingEnd (const char aa1, const char aa2) const | 
|  | returns if an enzyme will cut after first character  More... 
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|  | SuffixArraySeqan (const String &st, const String &filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO) | 
|  | constructor  More... 
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|  | SuffixArraySeqan (const SuffixArraySeqan &source) | 
|  | copy constructor  More... 
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| virtual | ~SuffixArraySeqan () | 
|  | destructor  More... 
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| String | toString () | 
|  | converts suffix array to a printable string  More... 
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| void | findSpec (std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &spec) | 
|  | the function that will find all peptide candidates for a given spectrum  More... 
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| bool | save (const String &filename) | 
|  | saves the suffix array to disc  More... 
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| bool | open (const String &filename) | 
|  | opens the suffix array  More... 
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| void | setTolerance (DoubleReal t) | 
|  | setter for tolerance  More... 
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| DoubleReal | getTolerance () const | 
|  | getter for tolerance  More... 
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| void | setTags (const std::vector< OpenMS::String > &tags) | 
|  | setter for tags  More... 
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| const std::vector < OpenMS::String > &
 | getTags () | 
|  | getter for tags  More... 
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| void | setUseTags (bool use_tags) | 
|  | setter for use_tags  More... 
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| bool | getUseTags () | 
|  | getter for use_tags  More... 
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| void | setNumberOfModifications (Size number_of_mods) | 
|  | setter for number of modifications  More... 
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| Size | getNumberOfModifications () | 
|  | getter for number of modifications  More... 
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| void | printStatistic () | 
|  | output for statistic  More... 
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|  | SuffixArray (const String &st, const String &filename) | 
|  | constructor taking the string and the filename for writing or reading  More... 
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|  | SuffixArray (const SuffixArray &sa) | 
|  | copy constructor  More... 
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| virtual | ~SuffixArray ()=0 | 
|  | destructor  More... 
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|  | SuffixArray () | 
|  | constructor  More... 
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|  | WeightWrapper () | 
|  | constructor  More... 
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|  | WeightWrapper (const WEIGHTMODE weight_mode) | 
|  | constructor  More... 
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| virtual | ~WeightWrapper () | 
|  | destructor  More... 
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|  | WeightWrapper (const WeightWrapper &source) | 
|  | copy constructor  More... 
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| void | setWeightMode (const WEIGHTMODE mode) | 
|  | Sets the weight mode (MONO or AVERAGE)  More... 
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| WEIGHTMODE | getWeightMode () const | 
|  | Gets the weight mode (MONO or AVERAGE)  More... 
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| DoubleReal | getWeight (const AASequence &aa) const | 
|  | returns the weight of either mono or average value  More... 
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| DoubleReal | getWeight (const EmpiricalFormula &ef) const | 
|  | returns the weight of either mono or average value  More... 
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| DoubleReal | getWeight (const Residue &r, Residue::ResidueType res_type=Residue::Full) const | 
|  | returns the weight of either mono or average value  More... 
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| enum | WEIGHTMODE { AVERAGE = 0, 
MONO, 
SIZE_OF_WEIGHTMODE
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| void | goNextSubTree_ (TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map) | 
|  | overwriting goNextSubTree_ from seqan index_esa_stree.h for mass update during suffix array traversal  More... 
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| void | goNextSubTree_ (TIter &it) | 
|  | goes to the next sub tree  More... 
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| void | goNext_ (TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map) | 
|  | overwriting goNext from seqan index_esa_stree.h for mass update during suffix array traversal  More... 
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| void | parseTree_ (TIter &it, std::vector< std::pair< SignedSize, SignedSize > > &out_number, std::vector< std::pair< SignedSize, SignedSize > > &edge_length, std::vector< SignedSize > &leafe_depth) | 
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| SignedSize | findFirst_ (const std::vector< DoubleReal > &spec, DoubleReal &m) | 
|  | binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance.  More... 
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| SignedSize | findFirst_ (const std::vector< DoubleReal > &spec, DoubleReal &m, SignedSize start, SignedSize end) | 
|  | binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance. it searches recursivly.  More... 
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| TIndex | index_ | 
|  | seqan suffix array  More... 
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| TIter * | it_ | 
|  | seqan suffix array iterator  More... 
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| const String & | s_ | 
|  | reference to strings for which the suffix array is build  More... 
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| DoubleReal | masse_ [255] | 
|  | amino acid masses  More... 
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| SignedSize | number_of_modifications_ | 
|  | number of allowed modifications  More... 
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| std::vector< String > | tags_ | 
|  | all tags  More... 
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| bool | use_tags_ | 
|  | if tags are used  More... 
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| DoubleReal | tol_ | 
|  | tolerance  More... 
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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.