IAlphabet Interface

IAlphabet Interface

An alphabet defines a set of symbols common to a particular representation of a biological sequence. The symbols in these alphabets are those you would find as the individual sequence items in an ISequence variable.

The symbols in an alphabet may represent a particular biological structure or they may represent information helpful in understanding a sequence. For instance gap symbol, termination symbol, and symbols representing items whose definition remains ambiguous are all allowed.

Namespace: Bio
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)

Syntax

C++

Copy

public interface IAlphabet : IEnumerable<byte>, 
	IEnumerable

Public Interface IAlphabet
	Inherits IEnumerable(Of Byte), IEnumerable

public interface class IAlphabet : IEnumerable<unsigned char>, 
	IEnumerable

type IAlphabet =  
    interface
        interface IEnumerable<byte>
        interface IEnumerable
    end

The IAlphabet type exposes the following members.

Properties

	Name	Description
	Count	Gets the count of symbols present in this alphabet. This includes basic symbols, gaps, terminations and ambiguous symbols present in this alphabet.
	HasAmbiguity	Gets a value indicating whether the alphabet has one or more symbols that represent an ambiguous item (i.e. and item for which it is not precisely known what it represents).
	HasGaps	Gets a value indicating whether the alphabet has one or more symbols that represent a gap.
	HasTerminations	Gets a value indicating whether the alphabet has one or more symbols that represent terminal items.
	IsComplementSupported	Gets a value indicating whether this alphabet supports complement or not.
	Item	Provides array like access to the symbols in this alphabet.
	Name	Gets a human readable name for the alphabet. For example "DNA", "RNA", or "Amino Acid".

Top

Methods

	Name	Description
	CheckIsAmbiguous	Checks if the provided item is an ambiguous character or not
	CheckIsGap	Checks if the provided item is a gap character or not
	CompareSymbols	Compares two items and specifies whether they are same or not. If the any of the bytes (Nucleotides) passed not belongs to this alphabet then this method throws an exception. TO Address scenarios like, N!=N, M != A etc. For the Scenarios like A == a, g == G use IsValidSymbol method.
	GetAmbiguousSymbols	Gets the ambiguous symbols present in alphabet.
	GetConsensusSymbol	Find the consensus symbol for a set of symbols.
	GetEnumerator	Returns an enumerator that iterates through the collection. (Inherited from IEnumerableByte.)
	GetFriendlyName	Gets the friendly name of a given symbol.
	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.
	GetValidSymbols	Gets the symbols that are valid for this alphabet. This Method can be used for better performance where lot of validation happens like in case of Parsers.
	TryGetAmbiguousSymbol	Gets the ambiguous symbol for the specified set of symbols.
	TryGetBasicSymbols	Gets the set of basic symbols for the specified ambiguous symbol.
	TryGetComplementSymbol(Byte, Byte)	Gets the complement for the specified symbol. This is to address the scenarios like in case of DNA complement of A is T etc. Note: If the complement is not supported then this method returns false. To know whether this alphabet supports complement or not, Use IsComplementSupported property.
	TryGetComplementSymbol(Byte, Byte)	Gets the complements for the specified symbols. This is to address the scenarios like in case of DNA complement of A is T etc. Note: If the complement is not supported then this method returns false. To know whether this alphabet supports complement or not, Use IsComplementSupported property.
	TryGetDefaultGapSymbol	Gets the default gap symbol if present in the alphabet.
	TryGetDefaultTerminationSymbol	Gets the default termination symbol if present in the alphabet.
	TryGetGapSymbols	Gets the gap symbols if present in the alphabet.
	TryGetTerminationSymbols	Gets the termination symbols if present in the alphabet.
	ValidateSequence	Validates if all symbols match with the specified alphabet type.

Top

Extension Methods

	Name	Description
	AppendByte(Byte)	Overloaded. Yield an Enumeration of the list with the item appended to the end (Defined by IEnumerableExtensions.)
	AppendByte(IEnumerableByte)	Overloaded. Yield a concatenation of the two Enumerable lists (Defined by IEnumerableExtensions.)
	CheckIsAmbiguous	Checks if the provided item is an ambiguous character or not (Defined by AlphabetExtensions.)
	CheckIsGap	Checks if the provided item is a gap character or not (Defined by AlphabetExtensions.)
	CheckIsTermination(Byte)	Overloaded. This returns true/false if the given symbol value is considered a termination value in the alphabet. (Defined by AlphabetExtensions.)
	CheckIsTermination(Char)	Overloaded. This returns true/false if the given symbol value is considered a termination value in the alphabet. (Defined by AlphabetExtensions.)
	ElementAtByte	Returns the element at a specified index in a sequence. (Defined by IEnumerableExtensions.)
	ForEachByte(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.)
	ForEachByte(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.)
	GetFriendlyName	Gets the friendly name of a given symbol. (Defined by AlphabetExtensions.)
	GetMummerAlphabet	Find corresponding mummer alphabet which supports the concatenation symbol using an existing alphabet (Defined by MummerAlphabetExtensions.)
	ShuffleByte	Shuffles the elements of a sequence. (Defined by IEnumerableExtensions.)
	StringJoin	Overloaded. Creates a string from a sequence of elements. No delimiter is used. (Defined by IEnumerableExtensions.)
	StringJoin(String)	Overloaded. Creates a delimited string from a sequence of elements. (Defined by IEnumerableExtensions.)
	StringJoin(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.)
	SubSequenceByte	Take the items from a sequence starting with item # start (index 0) and contining for count items. (Defined by IEnumerableExtensions.)
	ToHashSetByte	Overloaded. Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created. (Defined by IEnumerableExtensions.)
	ToHashSetByte(IEqualityComparerByte)	Overloaded. Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created. (Defined by IEnumerableExtensions.)
	ToQueueByte	Creates a Queue from a sequence. If the sequence is already a Queue, a new Queue is still created. (Defined by IEnumerableExtensions.)

Top

Reference

Bio Namespace