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RnaAlphabet Class
The basic alphabet that describes symbols used in RNA sequences. This alphabet allows not only for the four base nucleotide symbols, but also for various ambiguities, termination, and gap symbols.

The symbol representations come from the NCBI4na standard and are used in many sequence file formats. The NCBI4na standard is the same as the IUPACna standard with only the addition of the gap symbol.

The entries in this dictionary are: Symbol - Name A - Adenine C - Cytosine M - A or C G - Guanine R - G or A S - G or C V - G or V or A U - Uracil W - A or U Y - U or C H - A or C or U K - G or U D - G or A or U B - G or U or C - - Gap N - A or G or U or C.

Inheritance Hierarchy

Namespace: Bio
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
Syntax
public class RnaAlphabet : IAlphabet, 
	IEnumerable<byte>, IEnumerable

The RnaAlphabet type exposes the following members.

Constructors
  NameDescription
Protected methodRnaAlphabet
Initializes a new instance of the RnaAlphabet class.
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Properties
  NameDescription
Public propertyA
Gets A - Adenine.
Public propertyC
Gets C - Cytosine.
Public propertyCount
Gets count of nucleotides.
Public propertyG
Gets G - Guanine.
Public propertyGap
Gets Default Gap symbol.
Public propertyHasAmbiguity
Gets or sets a value indicating whether this alphabet has ambiguous symbols. This alphabet does have ambiguous symbols.
Public propertyHasGaps
Gets or sets a value indicating whether this alphabet has a gap symbol. This alphabet does have a gap symbol.
Public propertyHasTerminations
Gets or sets a value indicating whether this alphabet has termination symbols. This alphabet does not have termination symbols.
Public propertyIsComplementSupported
Gets or sets a value indicating whether this Complement is supported on this Alphabet. This alphabet has support for complement.
Public propertyItem
Gets the byte value of item at the given index.
Public propertyName
Gets or sets Friendly name for Alphabet type.
Public propertyU
Gets U - Uracil.
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Methods
  NameDescription
Protected methodAddNucleotide
Verify whether the nucleotide value or other possible values already exist or not.
Public methodCheckIsAmbiguous
Checks if the provided item is an ambiguous character or not
Public methodCheckIsGap
Checks if the provided item is a gap character or not
Public methodCompareSymbols
Compares two symbols.
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.
Public methodGetConsensusSymbol
Find the consensus nucleotide for a set of nucleotides.
Public methodGetEnumerator
Byte array of nucleotides.
Public methodGetFriendlyName
Gets the friendly name of a given symbol.
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.
Public methodGetType
Gets the Type of the current instance.
(Inherited from Object.)
Public methodGetValidSymbols
Get the valid symbols in the alphabet.
Protected methodMapAmbiguousNucleotide
Maps the ambiguous nucleotide to the nucleotides it represents. For example ambiguous nucleotide M represents the basic nucleotides A or C.
Protected methodMapComplementNucleotide
Verify whether the nucleotides exist or not.
Protected methodMemberwiseClone
Creates a shallow copy of the current Object.
(Inherited from Object.)
Public methodToString
Converts the RNA Alphabets.
(Overrides ObjectToString.)
Public methodTryGetAmbiguousSymbol
Get the ambiguous symbols if present in the alphabet.
Public methodTryGetBasicSymbols
Get the basic symbols if present in the alphabet.
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complement of this symbol.
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complements for specified symbols.
Public methodTryGetDefaultGapSymbol
Try to get the default gap symbol.
Public methodTryGetDefaultTerminationSymbol
Get the termination symbols if present in the alphabet.
Public methodTryGetGapSymbols
Get the gap symbols if present in the alphabet.
Public methodTryGetTerminationSymbols
Get the termination symbols if present in the alphabet.
Public methodValidateSequence
Validates if all symbols provided are RNA symbols or not.
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Fields
  NameDescription
Public fieldStatic memberInstance
Static instance of this class.
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Extension Methods
  NameDescription
Public Extension MethodAppendByte(Byte)Overloaded.
Yield an Enumeration of the list with the item appended to the end
(Defined by IEnumerableExtensions.)
Public Extension MethodAppendByte(IEnumerableByte)Overloaded.
Yield a concatenation of the two Enumerable lists
(Defined by IEnumerableExtensions.)
Public Extension MethodCheckIsAmbiguous
Checks if the provided item is an ambiguous character or not
(Defined by AlphabetExtensions.)
Public Extension MethodCheckIsGap
Checks if the provided item is a gap character or not
(Defined by AlphabetExtensions.)
Public Extension MethodCheckIsTermination(Byte)Overloaded.
This returns true/false if the given symbol value is considered a termination value in the alphabet.
(Defined by AlphabetExtensions.)
Public Extension MethodCheckIsTermination(Char)Overloaded.
This returns true/false if the given symbol value is considered a termination value in the alphabet.
(Defined by AlphabetExtensions.)
Public Extension MethodElementAtByte
Returns the element at a specified index in a sequence.
(Defined by IEnumerableExtensions.)
Public Extension MethodForEachByte(ActionByte)Overloaded.
Calls an action on each element of a sequence. The action takes one argument: an element. It has no return value.
(Defined by IEnumerableExtensions.)
Public Extension MethodForEachByte(ActionByte, Int32)Overloaded.
Calls an action on each element of a sequence. The action takes two arguments: an element and the index of the element. It has no return value.
(Defined by IEnumerableExtensions.)
Public Extension MethodGetFriendlyName
Gets the friendly name of a given symbol.
(Defined by AlphabetExtensions.)
Public Extension MethodGetMummerAlphabet
Find corresponding mummer alphabet which supports the concatenation symbol using an existing alphabet
(Defined by MummerAlphabetExtensions.)
Public Extension MethodShuffleByte
Shuffles the elements of a sequence.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoinOverloaded.
Creates a string from a sequence of elements. No delimiter is used.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoin(String)Overloaded.
Creates a delimited string from a sequence of elements.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoin(String, Int32, String)Overloaded.
Creates a delimited string from a sequence of elements. At most maxLength elements will be used and "..." shows that more elements were in the list.
(Defined by IEnumerableExtensions.)
Public Extension MethodSubSequenceByte
Take the items from a sequence starting with item # start (index 0) and contining for count items.
(Defined by IEnumerableExtensions.)
Public Extension MethodToHashSetByteOverloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.)
Public Extension MethodToHashSetByte(IEqualityComparerByte)Overloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.)
Public Extension MethodToQueueByte
Creates a Queue from a sequence. If the sequence is already a Queue, a new Queue is still created.
(Defined by IEnumerableExtensions.)
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See Also

Reference