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OpenMS
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Class for the enzymatic digestion of RNAs. More...
#include <OpenMS/CHEMISTRY/RNaseDigestion.h>
Public Member Functions | |
| void | setEnzyme (const DigestionEnzyme *enzyme) override |
| Sets the enzyme for the digestion. More... | |
| void | setEnzyme (const String &name) |
| Sets the enzyme for the digestion (by name) More... | |
| 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... | |
| void | digest (IdentificationData &id_data, Size min_length=0, Size max_length=0) const |
Performs the enzymatic digestion of all RNA parent sequences in IdentificationData. More... | |
 Public Member Functions inherited from EnzymaticDigestion | |
| EnzymaticDigestion () | |
| Default constructor. More... | |
| EnzymaticDigestion (const EnzymaticDigestion &rhs) | |
| Copy constructor. More... | |
| EnzymaticDigestion & | operator= (const EnzymaticDigestion &rhs) |
| Assignment operator. More... | |
| virtual | ~EnzymaticDigestion () |
| Destructor. More... | |
| Size | getMissedCleavages () const |
| Returns the number of missed cleavages for the digestion. More... | |
| 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... | |
| String | getEnzymeName () const |
| Returns the enzyme for the digestion. More... | |
| Specificity | getSpecificity () const |
| Returns the specificity for the digestion. More... | |
| void | setSpecificity (Specificity spec) |
| Sets the specificity for the digestion (default is SPEC_FULL). More... | |
| 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... | |
| 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... | |
| bool | isValidProduct (const String &protein, int pep_pos, int pep_length, bool ignore_missed_cleavages=true) const |
Is the peptide fragment starting at position pep_pos with length pep_length within the sequence protein generated by the current enzyme? More... | |
| Size | countInternalCleavageSites (const String &sequence) const |
| Counts the number of internal cleavage sites (missed cleavages) in a protein sequence. More... | |
| bool | filterByMissedCleavages (const String &sequence, const std::function< bool(const Int)> &filter) const |
| Filter based on the number of missed cleavages. More... | |
Protected Member Functions | |
| 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... | |
| Protected Member Functions inherited from EnzymaticDigestion | |
| 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... | |
| std::vector< int > | tokenize_ (const String &sequence, int start=0, int end=-1) const |
| Digests the sequence using the enzyme's regular expression. More... | |
| 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... | |
| 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 |
| 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... | |
Protected Attributes | |
| const Ribonucleotide * | five_prime_gain_ |
| 5' mod added by the enzyme More... | |
| const Ribonucleotide * | three_prime_gain_ |
| 3' mod added by the enzyme More... | |
| std::vector< boost::regex > | cuts_after_regexes_ |
| a vector of reg. exp. for enzyme cutting pattern, each regex represents a single nucleotide More... | |
| std::vector< boost::regex > | cuts_before_regexes_ |
| a vector reg. exp. for enzyme cutting pattern More... | |
| Protected Attributes inherited from EnzymaticDigestion | |
| Size | missed_cleavages_ |
| Number of missed cleavages. More... | |
| const DigestionEnzyme * | enzyme_ |
| Used enzyme. More... | |
| std::unique_ptr< boost::regex > | re_ |
| Regex for tokenizing (huge speedup by making this a member instead of stack object in tokenize_()) More... | |
| Specificity | specificity_ |
| specificity of enzyme More... | |
Additional Inherited Members | |
| Public Types inherited from EnzymaticDigestion | |
| enum | Specificity { SPEC_NONE = 0 , SPEC_SEMI = 1 , SPEC_FULL = 2 , SPEC_UNKNOWN = 3 , SPEC_NOCTERM = 8 , SPEC_NONTERM = 9 , SIZE_OF_SPECIFICITY = 10 } |
| when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important More... | |
| Static Public Member Functions inherited from EnzymaticDigestion | |
| static Specificity | getSpecificityByName (const String &name) |
| Static Public Attributes inherited from EnzymaticDigestion | |
| static const std::string | NamesOfSpecificity [SIZE_OF_SPECIFICITY] |
| Names of the Specificity. More... | |
| static const std::string | NoCleavage |
| Name for no cleavage. More... | |
| static const std::string | UnspecificCleavage |
| Name for unspecific cleavage. More... | |
Class for the enzymatic digestion of RNAs.
| void digest | ( | const NASequence & | rna, |
| std::vector< NASequence > & | output, | ||
| Size | min_length = 0, |
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| Size | max_length = 0 |
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| ) | const |
Performs the enzymatic digestion of a (potentially modified) RNA.
Only fragments of appropriate length (between min_length and max_length) are returned.
Referenced by NucleicAcidSearchEngine::main_().
| void digest | ( | IdentificationData & | id_data, |
| Size | min_length = 0, |
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| Size | max_length = 0 |
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| ) | const |
Performs the enzymatic digestion of all RNA parent sequences in IdentificationData.
Digestion products are stored as IdentifiedOligos with corresponding ParentMatch annotations. Only fragments of appropriate length (between min_length and max_length) are included.
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protected |
Returns the positions of digestion products in the RNA as pairs: (start, length)
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overridevirtual |
Sets the enzyme for the digestion.
Reimplemented from EnzymaticDigestion.
Referenced by NucleicAcidSearchEngine::main_().
| void setEnzyme | ( | const String & | name | ) |
Sets the enzyme for the digestion (by name)
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protected |
a vector of reg. exp. for enzyme cutting pattern, each regex represents a single nucleotide
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protected |
a vector reg. exp. for enzyme cutting pattern
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protected |
5' mod added by the enzyme
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protected |
3' mod added by the enzyme
1.9.1 
