DnaAlphabet Class |
The character 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 character.
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 T - Thymine W - A or T Y - T or C H - A or C or T K - G or T D - G or A or T B - G or T or C - - Gap N - A or G or T or C.
Namespace: Bio
The DnaAlphabet type exposes the following members.
Name | Description | |
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DnaAlphabet |
Initializes a new instance of the DnaAlphabet class.
|
Name | Description | |
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A |
Gets A - Adenine.
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C |
Gets C - Cytosine.
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Count |
Gets count of nucleotides.
| |
G |
Gets G - Guanine.
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Gap |
Gets Default Gap symbol.
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HasAmbiguity |
Gets or sets a value indicating whether this alphabet has ambiguous character.
This alphabet does have ambiguous symbols.
| |
HasGaps |
Gets or sets a value indicating whether this alphabet has a gap character.
This alphabet does have a gap symbol.
| |
HasTerminations |
Gets or sets a value indicating whether this alphabet has termination character.
This alphabet does not have termination symbols.
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IsComplementSupported |
Gets or sets a value indicating whether this Complement is supported on this Alphabet.
This alphabet has support for complement.
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Item |
Gets the byte value of item at the given index.
| |
Name |
Gets or sets Friendly name for Alphabet type.
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T |
Gets T - Thymine.
|
Name | Description | |
---|---|---|
AddNucleotide |
Add the given nucleotide symbols to this alphabet type.
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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 symbols.
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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.
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GetConsensusSymbol |
Find the consensus nucleotide for a set of nucleotides.
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GetEnumerator |
Byte array of nucleotides.
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GetFriendlyName |
Gets the friendly name of a given symbol.
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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.
| |
GetType | Gets the Type of the current instance. (Inherited from Object.) | |
GetValidSymbols |
Get the valid symbols in the alphabet.
| |
MapAmbiguousNucleotide |
Maps the ambiguous nucleotide to the nucleotides it represents.
For example ambiguous nucleotide M represents the basic nucleotides A or C.
| |
MapComplementNucleotide |
Verify whether the nucleotides exist or not.
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MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) | |
ToString |
Converts the DNA Alphabets to string.
(Overrides ObjectToString.) | |
TryGetAmbiguousSymbol |
Get the ambiguous symbols if present in the alphabet.
| |
TryGetBasicSymbols |
Get the basic symbols if present in the alphabet.
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TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complement of this symbol.
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TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complements for specified symbols.
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TryGetDefaultGapSymbol |
Try to get the default gap symbol.
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TryGetDefaultTerminationSymbol |
Get the termination symbols if present in the alphabet.
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TryGetGapSymbols |
Get the gap symbols if present in the alphabet.
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TryGetTerminationSymbols |
Get the termination symbols if present in the alphabet.
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ValidateSequence |
Validates if all symbols provided are DNA symbols or not.
|
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.) |