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MummerRnaAlphabet Class
Alphabet for use by MUMmer to support concatenation character '+'
Inheritance Hierarchy

Namespace: Bio.Algorithms.MUMmer
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
Syntax
public class MummerRnaAlphabet : AmbiguousRnaAlphabet

The MummerRnaAlphabet type exposes the following members.

Constructors
  NameDescription
Protected methodMummerRnaAlphabet
Initializes a new instance of the AmbiguousDnaAlphabet class.
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Properties
  NameDescription
Public propertyA
Gets A - Adenine.
(Inherited from RnaAlphabet.)
Public propertyAC
Gets Ambiguous symbols A-Adenine C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyACU
Gets Ambiguous symbols A-Adenine C-Cytosine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyAny
Gets Ambiguous symbol Any.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyAU
Gets Ambiguous symbols A-Adenine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyC
Gets C - Cytosine.
(Inherited from RnaAlphabet.)
Public propertyConcatenationChar
Gets the Concatenation character
Public propertyCount
Gets count of nucleotides.
(Inherited from RnaAlphabet.)
Public propertyG
Gets G - Guanine.
(Inherited from RnaAlphabet.)
Public propertyGA
Gets Ambiguous symbols G-Guanine A-Adenine.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyGap
Gets Default Gap symbol.
(Inherited from RnaAlphabet.)
Public propertyGAU
Gets Ambiguous symbols G-Guanine A-Adenine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyGC
Gets Ambiguous symbols G-Guanine C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyGCA
Gets Ambiguous symbols G-Guanine C-Cytosine A-Adenine.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyGU
Gets Ambiguous symbols G-Guanine U-Uracil.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyGUC
Gets Ambiguous symbols G-Guanine U-Uracil C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.)
Public propertyHasAmbiguity
Gets or sets a value indicating whether this alphabet has ambiguous symbols. This alphabet does have ambiguous symbols.
(Inherited from RnaAlphabet.)
Public propertyHasGaps
Gets or sets a value indicating whether this alphabet has a gap symbol. This alphabet does have a gap symbol.
(Inherited from RnaAlphabet.)
Public propertyHasTerminations
Gets or sets a value indicating whether this alphabet has termination symbols. This alphabet does not have termination symbols.
(Inherited from RnaAlphabet.)
Public propertyIsComplementSupported
Gets or sets a value indicating whether this Complement is supported on this Alphabet. This alphabet has support for complement.
(Inherited from RnaAlphabet.)
Public propertyItem
Gets the byte value of item at the given index.
(Inherited from RnaAlphabet.)
Public propertyName
Gets or sets Friendly name for Alphabet type.
(Inherited from RnaAlphabet.)
Public propertyU
Gets U - Uracil.
(Inherited from RnaAlphabet.)
Public propertyUC
Gets Ambiguous symbols U-Uracil C-Cytosine.
(Inherited from AmbiguousRnaAlphabet.)
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Methods
  NameDescription
Protected methodAddNucleotide
Verify whether the nucleotide value or other possible values already exist or not.
(Inherited from RnaAlphabet.)
Public methodCheckIsAmbiguous
Checks if the provided item is an ambiguous character or not
(Inherited from RnaAlphabet.)
Public methodCheckIsGap
Checks if the provided item is a gap character or not
(Inherited from RnaAlphabet.)
Public methodCompareSymbols
Compares two symbols.
(Inherited from RnaAlphabet.)
Public methodEquals
Determines whether the specified object is equal to the current object.
(Inherited from Object.)
Protected methodFinalize
Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection.
(Inherited from Object.)
Public methodGetAmbiguousSymbols
Gets the ambiguous symbols present in alphabet.
(Inherited from RnaAlphabet.)
Public methodGetConsensusSymbol
Find the consensus nucleotide for a set of nucleotides.
(Inherited from AmbiguousRnaAlphabet.)
Public methodGetEnumerator
Byte array of nucleotides.
(Inherited from RnaAlphabet.)
Public methodGetFriendlyName
Gets the friendly name of a given symbol.
(Inherited from RnaAlphabet.)
Public methodGetHashCode
Serves as the default hash function.
(Inherited from Object.)
Public methodGetSymbolValueMap
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.)
Public methodGetType
Gets the Type of the current instance.
(Inherited from Object.)
Public methodGetValidSymbols
Get the valid symbols in the alphabet.
(Inherited from RnaAlphabet.)
Protected methodMapAmbiguousNucleotide
Maps the ambiguous nucleotide to the nucleotides it represents. For example ambiguous nucleotide M represents the basic nucleotides A or C.
(Inherited from RnaAlphabet.)
Protected methodMapComplementNucleotide
Verify whether the nucleotides exist or not.
(Inherited from RnaAlphabet.)
Protected methodMemberwiseClone
Creates a shallow copy of the current Object.
(Inherited from Object.)
Public methodToString
Converts the RNA Alphabets.
(Inherited from RnaAlphabet.)
Public methodTryGetAmbiguousSymbol
Get the ambiguous symbols if present in the alphabet.
(Inherited from RnaAlphabet.)
Public methodTryGetBasicSymbols
Get the basic symbols if present in the alphabet.
(Inherited from RnaAlphabet.)
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complement of this symbol.
(Inherited from RnaAlphabet.)
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complements for specified symbols.
(Inherited from RnaAlphabet.)
Public methodTryGetDefaultGapSymbol
Try to get the default gap symbol.
(Inherited from RnaAlphabet.)
Public methodTryGetDefaultTerminationSymbol
Get the termination symbols if present in the alphabet.
(Inherited from RnaAlphabet.)
Public methodTryGetGapSymbols
Get the gap symbols if present in the alphabet.
(Inherited from RnaAlphabet.)
Public methodTryGetTerminationSymbols
Get the termination symbols if present in the alphabet.
(Inherited from RnaAlphabet.)
Public methodValidateSequence
Validates if all symbols provided are RNA symbols or not.
(Inherited from RnaAlphabet.)
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Fields
  NameDescription
Public fieldStatic memberInstance
New instance of Ambiguous symbol.
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See Also