| SAMDnaAlphabet Class |
SAM Dna Alphabet, Supports "=ACMGRSVTWYHKDBN." symbols.
Inheritance HierarchyNamespace: Bio.IO.SAM
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe SAMDnaAlphabet type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | SAMDnaAlphabet |
Initializes a new instance of the SAMDnaAlphabet class.
|
Properties| Name | Description | |
|---|---|---|
 | A |
Gets A - Adenine.
(Inherited from DnaAlphabet.) |
| AC |
Gets Ambiguous symbol A-Adenine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.) |
| ACT |
Gets Ambiguous symbol A-Adenine C-Cytosine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.) |
| Any |
Gets Ambiguous symbol Any.
(Inherited from AmbiguousDnaAlphabet.) |
| AT |
Gets Ambiguous symbol A-Adenine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.) |
| C |
Gets C - Cytosine.
(Inherited from DnaAlphabet.) |
| Count |
Gets count of nucleotides.
(Inherited from DnaAlphabet.) |
| Dot |
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.
|
| Equal |
Gets the SAM symbol "=" (Equal to reference symbol)
|
| G |
Gets G - Guanine.
(Inherited from DnaAlphabet.) |
| GA |
Gets Ambiguous symbol G-Guanine A-Adenine.
(Inherited from AmbiguousDnaAlphabet.) |
| Gap |
Gets Default Gap symbol.
(Inherited from DnaAlphabet.) |
| GAT |
Gets Ambiguous symbol G-Guanine A-Adenine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.) |
| GC |
Gets Ambiguous symbol G-Guanine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.) |
| GCA |
Gets Ambiguous symbol G-Guanine C-Cytosine A-Adenine.
(Inherited from AmbiguousDnaAlphabet.) |
| GT |
Gets Ambiguous symbol G-Guanine T-Thymine.
(Inherited from AmbiguousDnaAlphabet.) |
| GTC |
Gets Ambiguous symbol G-Guanine T-Thymine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.) |
| HasAmbiguity |
Gets or sets a value indicating whether this alphabet has ambiguous character.
This alphabet does have ambiguous symbols.
(Inherited from DnaAlphabet.) |
| HasGaps |
Gets or sets a value indicating whether this alphabet has a gap character.
This alphabet does have a gap symbol.
(Inherited from DnaAlphabet.) |
| HasTerminations |
Gets or sets a value indicating whether this alphabet has termination character.
This alphabet does not have termination symbols.
(Inherited from DnaAlphabet.) |
| IsComplementSupported |
Gets or sets a value indicating whether this Complement is supported on this Alphabet.
This alphabet has support for complement.
(Inherited from DnaAlphabet.) |
| Item |
Gets the byte value of item at the given index.
(Inherited from DnaAlphabet.) |
| Name |
Gets or sets Friendly name for Alphabet type.
(Inherited from DnaAlphabet.) |
| T |
Gets T - Thymine.
(Inherited from DnaAlphabet.) |
| TC |
Gets Ambiguous symbol T-Thymine C-Cytosine.
(Inherited from AmbiguousDnaAlphabet.) |
Methods| Name | Description | |
|---|---|---|
| AddNucleotide |
Add the given nucleotide symbols to this alphabet type.
(Inherited from DnaAlphabet.) |
 | CheckIsAmbiguous |
Checks if the provided item is an ambiguous character or not
Note: for '=' and '.' symbols this method returns false.
(Overrides DnaAlphabetCheckIsAmbiguous(Byte).) |
| CheckIsGap |
Checks if the provided item is a gap character or not
(Inherited from DnaAlphabet.) |
| CompareSymbols |
Compares two symbols.
(Inherited from DnaAlphabet.) |
| Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) |
| Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) |
| GetAmbiguousSymbols |
Gets the ambiguous symbols present in alphabet.
(Inherited from DnaAlphabet.) |
| GetConsensusSymbol |
Find the consensus nucleotide for a set of nucleotides.
(Inherited from AmbiguousDnaAlphabet.) |
| GetEnumerator |
Byte array of nucleotides.
(Inherited from DnaAlphabet.) |
| GetFriendlyName |
Gets the friendly name of a given symbol.
(Inherited from DnaAlphabet.) |
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| 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.
(Inherited from DnaAlphabet.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| GetValidSymbols |
Get the valid symbols in the alphabet.
(Inherited from DnaAlphabet.) |
| MapAmbiguousNucleotide |
Maps the ambiguous nucleotide to the nucleotides it represents.
For example ambiguous nucleotide M represents the basic nucleotides A or C.
(Inherited from DnaAlphabet.) |
| MapComplementNucleotide |
Verify whether the nucleotides exist or not.
(Inherited from DnaAlphabet.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ToString |
Converts the DNA Alphabets to string.
(Inherited from DnaAlphabet.) |
| TryGetAmbiguousSymbol |
Get the ambiguous symbols if present in the alphabet.
(Inherited from DnaAlphabet.) |
| TryGetBasicSymbols |
Get the basic symbols if present in the alphabet.
(Inherited from DnaAlphabet.) |
| TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complement of this symbol.
(Inherited from DnaAlphabet.) |
| TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complements for specified symbols.
(Inherited from DnaAlphabet.) |
| TryGetDefaultGapSymbol |
Try to get the default gap symbol.
(Inherited from DnaAlphabet.) |
| TryGetDefaultTerminationSymbol |
Get the termination symbols if present in the alphabet.
(Inherited from DnaAlphabet.) |
| TryGetGapSymbols |
Get the gap symbols if present in the alphabet.
(Inherited from DnaAlphabet.) |
| TryGetTerminationSymbols |
Get the termination symbols if present in the alphabet.
(Inherited from DnaAlphabet.) |
| ValidateSequence |
Validates if all symbols provided are DNA symbols or not.
(Inherited from DnaAlphabet.) |
Fields
See Also