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.