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OpenMS
2.4.0
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OpenMS
2.4.0
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Class for the enzymatic digestion of RNAs. More...
#include <OpenMS/CHEMISTRY/RNaseDigestion.h>
Public Member Functions | |
| void | setEnzyme (const String &name) |
| Sets the enzyme for the digestion (by name) More... | |
| void | digest (const String &rna, std::vector< String > &output, Size min_length, Size max_length) const |
| Performs the enzymatic digestion of an RNA. More... | |
| void | setEnzyme (const DigestionEnzyme *enzyme) |
| Sets the enzyme for the digestion. More... | |
 Public Member Functions inherited from EnzymaticDigestion | |
| EnzymaticDigestion () | |
| Default constructor. 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... | |
| void | setEnzyme (const DigestionEnzyme *enzyme) |
| Sets 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... | |
| 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... | |
| bool | filterByMissedCleavages (const String &sequence, std::function< bool(const Int)> filter) const |
| Filter based on the number of missed cleavages. More... | |
Additional Inherited Members | |
| Public Types inherited from EnzymaticDigestion | |
| enum | Specificity { SPEC_FULL, SPEC_SEMI, SPEC_NONE, SIZE_OF_SPECIFICITY } |
| 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 | UnspecificCleavage |
| Name for unspecific cleavage. 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 | 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 inherited from EnzymaticDigestion | |
| Size | missed_cleavages_ |
| Number of missed cleavages. More... | |
| const DigestionEnzyme * | enzyme_ |
| Used enzyme. More... | |
| 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... | |
Class for the enzymatic digestion of RNAs.
| void digest | ( | const String & | rna, |
| std::vector< String > & | output, | ||
| Size | min_length, | ||
| Size | max_length | ||
| ) | const |
Performs the enzymatic digestion of an RNA.
Only fragments of appropriate length (between min_length and max_length) are returned.
There are two complications: 1. The original RNA may have terminal phosphates ("p"), which we want to ignore, but not remove. 2. The enzyme may add modifications (e.g. "p") on the 5' or 3' ends of cleavage products, but NOT on the original 5' or 3' ends of the RNA.
| void setEnzyme |
Sets the enzyme for the digestion.
| void setEnzyme | ( | const String & | name | ) |
Sets the enzyme for the digestion (by name)
1.8.14