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void | setEnzyme (const DigestionEnzyme *enzyme) override |
| Sets the enzyme for the digestion. More...
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void | setEnzyme (const String &name) |
| Sets the enzyme for the digestion (by name) More...
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void | digest (const NASequence &rna, std::vector< NASequence > &output, Size min_length=0, Size max_length=0) const |
| Performs the enzymatic digestion of a (potentially modified) RNA. More...
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void | digest (IdentificationData &id_data, Size min_length=0, Size max_length=0) const |
| Performs the enzymatic digestion of all RNA parent molecules in IdentificationData . More...
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| EnzymaticDigestion () |
| Default constructor. More...
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virtual | ~EnzymaticDigestion () |
| Destructor. More...
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Size | getMissedCleavages () const |
| Returns the number of missed cleavages for the digestion. More...
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void | setMissedCleavages (Size missed_cleavages) |
| Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used. More...
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String | getEnzymeName () const |
| Returns the enzyme for the digestion. More...
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Specificity | getSpecificity () const |
| Returns the specificity for the digestion. More...
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void | setSpecificity (Specificity spec) |
| Sets the specificity for the digestion (default is SPEC_FULL). More...
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Size | digestUnmodified (const StringView &sequence, std::vector< StringView > &output, Size min_length=1, Size max_length=0) const |
| Performs the enzymatic digestion of an unmodified sequence. More...
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Size | digestUnmodified (const StringView &sequence, std::vector< std::pair< Size, Size >> &output, Size min_length=1, Size max_length=0) const |
| Performs the enzymatic digestion of an unmodified sequence. More...
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bool | isValidProduct (const String &sequence, int pos, int length, bool ignore_missed_cleavages=true) const |
| Is the peptide fragment starting at position pos with length length within the sequence sequence generated by the current enzyme? More...
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bool | filterByMissedCleavages (const String &sequence, std::function< bool(const Int)> filter) const |
| Filter based on the number of missed cleavages. More...
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std::vector< std::pair< Size, Size > > | getFragmentPositions_ (const NASequence &rna, Size min_length, Size max_length) const |
| Returns the positions of digestion products in the RNA as pairs: (start, length) More...
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bool | isValidProduct_ (const String &sequence, int pos, int length, bool ignore_missed_cleavages, bool allow_nterm_protein_cleavage, bool allow_random_asp_pro_cleavage) const |
| supports functionality for ProteaseDigestion as well (which is deeply weaved into the function) To avoid code duplication, this is stored here and called by wrappers. Do not duplicate the code, just for the sake of semantics (unless we can come up with a clean separation) Note: the overhead of allow_nterm_protein_cleavage and allow_random_asp_pro_cleavage is marginal; the main runtime is spend during tokenize_() More...
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std::vector< int > | tokenize_ (const String &sequence, int start=0, int end=-1) const |
| Digests the sequence using the enzyme's regular expression. More...
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Size | digestAfterTokenize_ (const std::vector< int > &fragment_positions, const StringView &sequence, std::vector< StringView > &output, Size min_length=0, Size max_length=-1) const |
| Helper function for digestUnmodified() More...
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Size | digestAfterTokenize_ (const std::vector< int > &fragment_positions, const StringView &sequence, std::vector< std::pair< Size, Size >> &output, Size min_length=0, Size max_length=-1) const |
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Size | countMissedCleavages_ (const std::vector< int > &cleavage_positions, Size seq_start, Size seq_end) const |
| Counts the number of missed cleavages in a sequence fragment. More...
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Class for the enzymatic digestion of RNAs.
- See also
- DigestionEnzymeRNA