| MummerRnaAlphabet Class |
Alphabet for use by MUMmer to support concatenation character '+'
Inheritance HierarchyNamespace: Bio.Algorithms.MUMmer
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe MummerRnaAlphabet type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | MummerRnaAlphabet |
Initializes a new instance of the AmbiguousDnaAlphabet class.
|
Properties| Name | Description | |
|---|---|---|
 | A |
Gets A - Adenine.
(Inherited from RnaAlphabet.) |
| AC |
Gets Ambiguous symbols A-Adenine C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.) |
| ACU |
Gets Ambiguous symbols A-Adenine C-Cytosine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.) |
| Any |
Gets Ambiguous symbol Any.
(Inherited from AmbiguousRnaAlphabet.) |
| AU |
Gets Ambiguous symbols A-Adenine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.) |
| C |
Gets C - Cytosine.
(Inherited from RnaAlphabet.) |
| ConcatenationChar |
Gets the Concatenation character
|
| Count |
Gets count of nucleotides.
(Inherited from RnaAlphabet.) |
| G |
Gets G - Guanine.
(Inherited from RnaAlphabet.) |
| GA |
Gets Ambiguous symbols G-Guanine A-Adenine.
(Inherited from AmbiguousRnaAlphabet.) |
| Gap |
Gets Default Gap symbol.
(Inherited from RnaAlphabet.) |
| GAU |
Gets Ambiguous symbols G-Guanine A-Adenine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.) |
| GC |
Gets Ambiguous symbols G-Guanine C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.) |
| GCA |
Gets Ambiguous symbols G-Guanine C-Cytosine A-Adenine.
(Inherited from AmbiguousRnaAlphabet.) |
| GU |
Gets Ambiguous symbols G-Guanine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.) |
| GUC |
Gets Ambiguous symbols G-Guanine U-Uracil C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.) |
| HasAmbiguity |
Gets or sets a value indicating whether this alphabet has ambiguous symbols.
This alphabet does have ambiguous symbols.
(Inherited from RnaAlphabet.) |
| HasGaps |
Gets or sets a value indicating whether this alphabet has a gap symbol.
This alphabet does have a gap symbol.
(Inherited from RnaAlphabet.) |
| HasTerminations |
Gets or sets a value indicating whether this alphabet has termination symbols.
This alphabet does not have termination symbols.
(Inherited from RnaAlphabet.) |
| IsComplementSupported |
Gets or sets a value indicating whether this Complement is supported on this Alphabet.
This alphabet has support for complement.
(Inherited from RnaAlphabet.) |
| Item |
Gets the byte value of item at the given index.
(Inherited from RnaAlphabet.) |
| Name |
Gets or sets Friendly name for Alphabet type.
(Inherited from RnaAlphabet.) |
| U |
Gets U - Uracil.
(Inherited from RnaAlphabet.) |
| UC |
Gets Ambiguous symbols U-Uracil C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.) |
Methods| Name | Description | |
|---|---|---|
| AddNucleotide |
Verify whether the nucleotide value or other possible values already exist or not.
(Inherited from RnaAlphabet.) |
 | CheckIsAmbiguous |
Checks if the provided item is an ambiguous character or not
(Inherited from RnaAlphabet.) |
| CheckIsGap |
Checks if the provided item is a gap character or not
(Inherited from RnaAlphabet.) |
| CompareSymbols |
Compares two symbols.
(Inherited from RnaAlphabet.) |
| Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) |
| Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) |
| GetAmbiguousSymbols |
Gets the ambiguous symbols present in alphabet.
(Inherited from RnaAlphabet.) |
| GetConsensusSymbol |
Find the consensus nucleotide for a set of nucleotides.
(Inherited from AmbiguousRnaAlphabet.) |
| GetEnumerator |
Byte array of nucleotides.
(Inherited from RnaAlphabet.) |
| GetFriendlyName |
Gets the friendly name of a given symbol.
(Inherited from RnaAlphabet.) |
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetSymbolValueMap |
Maps A to A and a to A
that is key will contain unique values.
This will be used in the IsValidSymbol method to address Scenarios like a == A, G == g etc.
(Inherited from RnaAlphabet.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| GetValidSymbols |
Get the valid symbols in the alphabet.
(Inherited from RnaAlphabet.) |
| MapAmbiguousNucleotide |
Maps the ambiguous nucleotide to the nucleotides it represents.
For example ambiguous nucleotide M represents the basic nucleotides A or C.
(Inherited from RnaAlphabet.) |
| MapComplementNucleotide |
Verify whether the nucleotides exist or not.
(Inherited from RnaAlphabet.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ToString |
Converts the RNA Alphabets.
(Inherited from RnaAlphabet.) |
| TryGetAmbiguousSymbol |
Get the ambiguous symbols if present in the alphabet.
(Inherited from RnaAlphabet.) |
| TryGetBasicSymbols |
Get the basic symbols if present in the alphabet.
(Inherited from RnaAlphabet.) |
| TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complement of this symbol.
(Inherited from RnaAlphabet.) |
| TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complements for specified symbols.
(Inherited from RnaAlphabet.) |
| TryGetDefaultGapSymbol |
Try to get the default gap symbol.
(Inherited from RnaAlphabet.) |
| TryGetDefaultTerminationSymbol |
Get the termination symbols if present in the alphabet.
(Inherited from RnaAlphabet.) |
| TryGetGapSymbols |
Get the gap symbols if present in the alphabet.
(Inherited from RnaAlphabet.) |
| TryGetTerminationSymbols |
Get the termination symbols if present in the alphabet.
(Inherited from RnaAlphabet.) |
| ValidateSequence |
Validates if all symbols provided are RNA symbols or not.
(Inherited from RnaAlphabet.) |
Fields
See Also