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 >, double > > > &candidates, const std::vector< double > &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 (double t) |
| setter for tolerance More...
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double | 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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double | getWeight (const AASequence &aa) const |
| returns the weight of either mono or average value More...
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double | getWeight (const EmpiricalFormula &ef) const |
| returns the weight of either mono or average value More...
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double | 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, double &m, std::stack< double > &allm, std::stack< std::map< double, 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, double &m, std::stack< double > &allm, std::stack< std::map< double, 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< double > &spec, double &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< double > &spec, double &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 recursively. 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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double | 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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double | 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.