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SAMDnaAlphabet Class
SAM Dna Alphabet, Supports "=ACMGRSVTWYHKDBN." symbols.
Inheritance Hierarchy

Namespace: Bio.IO.SAM
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
Syntax
public class SAMDnaAlphabet : AmbiguousDnaAlphabet

The SAMDnaAlphabet type exposes the following members.

Constructors
  NameDescription
Protected methodSAMDnaAlphabet
Initializes a new instance of the SAMDnaAlphabet class.
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Properties
  NameDescription
Public propertyA
Gets A - Adenine.
(Inherited from DnaAlphabet.)
Public propertyAC
Gets Ambiguous symbol A-Adenine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyACT
Gets Ambiguous symbol A-Adenine C-Cytosine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyAny
Gets Ambiguous symbol Any.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyAT
Gets Ambiguous symbol A-Adenine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyC
Gets C - Cytosine.
(Inherited from DnaAlphabet.)
Public propertyCount
Gets count of nucleotides.
(Inherited from DnaAlphabet.)
Public propertyDot
Gets symbol "." (Space holder to represent Intron). As per the Specification Version 0.1.2-draft (20090820) and 1.4-r985 In a split alignment "..." represents Intron.
Public propertyEqual
Gets the SAM symbol "=" (Equal to reference symbol)
Public propertyG
Gets G - Guanine.
(Inherited from DnaAlphabet.)
Public propertyGA
Gets Ambiguous symbol G-Guanine A-Adenine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyGap
Gets Default Gap symbol.
(Inherited from DnaAlphabet.)
Public propertyGAT
Gets Ambiguous symbol G-Guanine A-Adenine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyGC
Gets Ambiguous symbol G-Guanine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyGCA
Gets Ambiguous symbol G-Guanine C-Cytosine A-Adenine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyGT
Gets Ambiguous symbol G-Guanine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyGTC
Gets Ambiguous symbol G-Guanine T-Thymine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.)
Public propertyHasAmbiguity
Gets or sets a value indicating whether this alphabet has ambiguous character. This alphabet does have ambiguous symbols.
(Inherited from DnaAlphabet.)
Public propertyHasGaps
Gets or sets a value indicating whether this alphabet has a gap character. This alphabet does have a gap symbol.
(Inherited from DnaAlphabet.)
Public propertyHasTerminations
Gets or sets a value indicating whether this alphabet has termination character. This alphabet does not have termination symbols.
(Inherited from DnaAlphabet.)
Public propertyIsComplementSupported
Gets or sets a value indicating whether this Complement is supported on this Alphabet. This alphabet has support for complement.
(Inherited from DnaAlphabet.)
Public propertyItem
Gets the byte value of item at the given index.
(Inherited from DnaAlphabet.)
Public propertyName
Gets or sets Friendly name for Alphabet type.
(Inherited from DnaAlphabet.)
Public propertyT
Gets T - Thymine.
(Inherited from DnaAlphabet.)
Public propertyTC
Gets Ambiguous symbol T-Thymine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.)
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Methods
  NameDescription
Protected methodAddNucleotide
Add the given nucleotide symbols to this alphabet type.
(Inherited from DnaAlphabet.)
Public methodCheckIsAmbiguous
Checks if the provided item is an ambiguous character or not Note: for '=' and '.' symbols this method returns false.
(Overrides DnaAlphabetCheckIsAmbiguous(Byte).)
Public methodCheckIsGap
Checks if the provided item is a gap character or not
(Inherited from DnaAlphabet.)
Public methodCompareSymbols
Compares two symbols.
(Inherited from DnaAlphabet.)
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 DnaAlphabet.)
Public methodGetConsensusSymbol
Find the consensus nucleotide for a set of nucleotides.
(Inherited from AmbiguousDnaAlphabet.)
Public methodGetEnumerator
Byte array of nucleotides.
(Inherited from DnaAlphabet.)
Public methodGetFriendlyName
Gets the friendly name of a given symbol.
(Inherited from DnaAlphabet.)
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 DnaAlphabet.)
Public methodGetType
Gets the Type of the current instance.
(Inherited from Object.)
Public methodGetValidSymbols
Get the valid symbols in the alphabet.
(Inherited from DnaAlphabet.)
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 DnaAlphabet.)
Protected methodMapComplementNucleotide
Verify whether the nucleotides exist or not.
(Inherited from DnaAlphabet.)
Protected methodMemberwiseClone
Creates a shallow copy of the current Object.
(Inherited from Object.)
Public methodToString
Converts the DNA Alphabets to string.
(Inherited from DnaAlphabet.)
Public methodTryGetAmbiguousSymbol
Get the ambiguous symbols if present in the alphabet.
(Inherited from DnaAlphabet.)
Public methodTryGetBasicSymbols
Get the basic symbols if present in the alphabet.
(Inherited from DnaAlphabet.)
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complement of this symbol.
(Inherited from DnaAlphabet.)
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complements for specified symbols.
(Inherited from DnaAlphabet.)
Public methodTryGetDefaultGapSymbol
Try to get the default gap symbol.
(Inherited from DnaAlphabet.)
Public methodTryGetDefaultTerminationSymbol
Get the termination symbols if present in the alphabet.
(Inherited from DnaAlphabet.)
Public methodTryGetGapSymbols
Get the gap symbols if present in the alphabet.
(Inherited from DnaAlphabet.)
Public methodTryGetTerminationSymbols
Get the termination symbols if present in the alphabet.
(Inherited from DnaAlphabet.)
Public methodValidateSequence
Validates if all symbols provided are DNA symbols or not.
(Inherited from DnaAlphabet.)
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Fields
  NameDescription
Public fieldStatic memberInstance
Singleton instance of SAMDnaAlphabet.
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See Also