Click or drag to resize
MummerProteinAlphabet 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 MummerProteinAlphabet : AmbiguousProteinAlphabet

The MummerProteinAlphabet type exposes the following members.

Constructors
  NameDescription
Protected methodMummerProteinAlphabet
Initializes a new instance of the AmbiguousDnaAlphabet class.
Top
Properties
  NameDescription
Public propertyA
Gets the Alanine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyB
Gets the Aspartic Acid or Asparagine.
(Inherited from AmbiguousProteinAlphabet.)
Public propertyC
Gets the Cysteine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyConcatenationChar
Gets the Concatenation character
Public propertyCount
Gets count of nucleotides.
(Inherited from ProteinAlphabet.)
Public propertyD
Gets the Aspartic Acid.
(Inherited from ProteinAlphabet.)
Public propertyE
Gets the Glutamic Acid.
(Inherited from ProteinAlphabet.)
Public propertyF
Gets the Phenylalanine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyG
Gets the Glycine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyGap
Gets the Gap character.
(Inherited from ProteinAlphabet.)
Public propertyH
Gets the Histidine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyHasAmbiguity
Gets or sets a value indicating whether this alphabet has ambiguous characters. This alphabet does have ambiguous characters.
(Inherited from ProteinAlphabet.)
Public propertyHasGaps
Gets or sets a value indicating whether this alphabet has a gap character. This alphabet does have a gap character.
(Inherited from ProteinAlphabet.)
Public propertyHasTerminations
Gets or sets a value indicating whether this alphabet has termination characters. This alphabet does have termination characters.
(Inherited from ProteinAlphabet.)
Public propertyI
Gets the Isoleucine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyIsComplementSupported
Gets or sets a value indicating whether complement is supported or not.
(Inherited from ProteinAlphabet.)
Public propertyItem
Gets the byte value of item at the given index.
(Inherited from ProteinAlphabet.)
Public propertyJ
Gets the Leucine or Isoleucine.
(Inherited from AmbiguousProteinAlphabet.)
Public propertyK
Gets the Lysine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyL
Gets the Leucine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyM
Gets the Methionine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyN
Gets the Asparagine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyName
Gets or sets the name of this alphabet - this is always 'Protein'.
(Inherited from ProteinAlphabet.)
Public propertyO
Gets the Pyrrolysine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyP
Gets the Proline Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyQ
Gets the Glutamine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyR
Gets the Arginine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyS
Gets the Serine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyT
Gets the Threoine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyTer
Gets the Termination character.
(Inherited from ProteinAlphabet.)
Public propertyU
Gets the Selenocysteine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyV
Gets the Valine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyW
Gets the Tryptophan Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyX
Gets X - Xxx - Undetermined or atypical.
(Inherited from AmbiguousProteinAlphabet.)
Public propertyY
Gets the Tyrosine Amino acid.
(Inherited from ProteinAlphabet.)
Public propertyZ
Gets Z - Glx - Glutamic Acid or Glutamine.
(Inherited from AmbiguousProteinAlphabet.)
Top
Methods
  NameDescription
Protected methodAddAminoAcid
Adds a Amino acid to the existing amino acids.
(Inherited from ProteinAlphabet.)
Public methodCheckIsAmbiguous
Checks if the provided item is an ambiguous character or not
(Inherited from ProteinAlphabet.)
Public methodCheckIsGap
Checks if the provided item is a gap character or not
(Inherited from ProteinAlphabet.)
Public methodCompareSymbols
Compares two symbols.
(Inherited from ProteinAlphabet.)
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 ambigious characters present in alphabet.
(Inherited from ProteinAlphabet.)
Public methodGetConsensusSymbol
Find the consensus nucleotide for a set of nucleotides.
(Inherited from AmbiguousProteinAlphabet.)
Public methodGetEnumerator
Byte array of nucleotides.
(Inherited from ProteinAlphabet.)
Public methodGetFriendlyName
Gets the friendly name of a given symbol.
(Inherited from ProteinAlphabet.)
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 ProteinAlphabet.)
Public methodGetType
Gets the Type of the current instance.
(Inherited from Object.)
Public methodGetValidSymbols
Gets the valid symbol.
(Inherited from ProteinAlphabet.)
Protected methodMapAmbiguousAminoAcid
Maps the ambiguous amino acids to the amino acids it represents. For example ambiguous amino acids M represents the basic nucleotides A or C.
(Inherited from ProteinAlphabet.)
Protected methodMemberwiseClone
Creates a shallow copy of the current Object.
(Inherited from Object.)
Public methodToString
Converts the Protein Alphabets to string.
(Inherited from ProteinAlphabet.)
Public methodTryGetAmbiguousSymbol
Gets the Ambiguous symbol.
(Inherited from ProteinAlphabet.)
Public methodTryGetBasicSymbols
Gets the Basic symbol.
(Inherited from ProteinAlphabet.)
Public methodTryGetComplementSymbol(Byte, Byte)
Gets the complement of the symbol.
(Inherited from ProteinAlphabet.)
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complements for specified symbols.
(Inherited from ProteinAlphabet.)
Public methodTryGetDefaultGapSymbol
Gets the default Gap symbol.
(Inherited from ProteinAlphabet.)
Public methodTryGetDefaultTerminationSymbol
Gets the default Termination symbol.
(Inherited from ProteinAlphabet.)
Public methodTryGetGapSymbols
Gets the Gap symbol.
(Inherited from ProteinAlphabet.)
Public methodTryGetTerminationSymbols
Gets the Termination symbol.
(Inherited from ProteinAlphabet.)
Public methodValidateSequence
Validates if all symbols provided are Protein symbols or not.
(Inherited from ProteinAlphabet.)
Top
Fields
  NameDescription
Public fieldStatic memberInstance
New instance of Ambiguous symbol.
Top
See Also