ProteinAlphabet Class |
The character representations come from the NCBIstdaa standard and are used in many sequence file formats. The NCBIstdaa standard has all the same characters as NCBIeaa and IUPACaa, but adds Selenocysteine, termination, and gap symbols to the latter.
The entries in this dictionary are: Symbol - Extended Symbol - Name A - Ala - Alanine C - Cys - Cysteine D - Asp - Aspartic Acid E - Glu - Glutamic Acid F - Phe - Phenylalanine G - Gly - Glycine H - His - Histidine I - Ile - Isoleucine K - Lys - Lysine L - Leu - Leucine M - Met - Methionine N - Asn - Asparagine O - Pyl - Pyrrolysine P - Pro - Proline Q - Gln - Glutamine R - Arg - Arginine S - Ser - Serine T - Thr - Threoine U - Sel - Selenocysteine V - Val - Valine W - Trp - Tryptophan Y - Tyr - Tyrosine * - Ter - Termination - - --- - Gap.
Namespace: Bio
The ProteinAlphabet type exposes the following members.
Name | Description | |
---|---|---|
ProteinAlphabet |
Initializes a new instance of the ProteinAlphabet class.
|
Name | Description | |
---|---|---|
A |
Gets the Alanine Amino acid.
| |
C |
Gets the Cysteine Amino acid.
| |
Count |
Gets count of nucleotides.
| |
D |
Gets the Aspartic Acid.
| |
E |
Gets the Glutamic Acid.
| |
F |
Gets the Phenylalanine Amino acid.
| |
G |
Gets the Glycine Amino acid.
| |
Gap |
Gets the Gap character.
| |
H |
Gets the Histidine Amino acid.
| |
HasAmbiguity |
Gets or sets a value indicating whether this alphabet has ambiguous characters.
This alphabet does have ambiguous characters.
| |
HasGaps |
Gets or sets a value indicating whether this alphabet has a gap character.
This alphabet does have a gap character.
| |
HasTerminations |
Gets or sets a value indicating whether this alphabet has termination characters.
This alphabet does have termination characters.
| |
I |
Gets the Isoleucine Amino acid.
| |
IsComplementSupported |
Gets or sets a value indicating whether complement is supported or not.
| |
Item |
Gets the byte value of item at the given index.
| |
K |
Gets the Lysine Amino acid.
| |
L |
Gets the Leucine Amino acid.
| |
M |
Gets the Methionine Amino acid.
| |
N |
Gets the Asparagine Amino acid.
| |
Name |
Gets or sets the name of this alphabet - this is always 'Protein'.
| |
O |
Gets the Pyrrolysine Amino acid.
| |
P |
Gets the Proline Amino acid.
| |
Q |
Gets the Glutamine Amino acid.
| |
R |
Gets the Arginine Amino acid.
| |
S |
Gets the Serine Amino acid.
| |
T |
Gets the Threoine Amino acid.
| |
Ter |
Gets the Termination character.
| |
U |
Gets the Selenocysteine Amino acid.
| |
V |
Gets the Valine Amino acid.
| |
W |
Gets the Tryptophan Amino acid.
| |
Y |
Gets the Tyrosine Amino acid.
|
Name | Description | |
---|---|---|
AddAminoAcid |
Adds a Amino acid to the existing amino acids.
| |
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.
| |
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 ambigious characters present in alphabet.
| |
GetConsensusSymbol |
Find the consensus nucleotide for a set of nucleotides.
| |
GetEnumerator |
Byte array of nucleotides.
| |
GetFriendlyName |
Gets the friendly name of a given symbol.
| |
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 |
Gets the valid symbol.
| |
MapAmbiguousAminoAcid |
Maps the ambiguous amino acids to the amino acids it represents.
For example ambiguous amino acids M represents the basic nucleotides A or C.
| |
MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) | |
ToString |
Converts the Protein Alphabets to string.
(Overrides ObjectToString.) | |
TryGetAmbiguousSymbol |
Gets the Ambiguous symbol.
| |
TryGetBasicSymbols |
Gets the Basic symbol.
| |
TryGetComplementSymbol(Byte, Byte) |
Gets the complement of the symbol.
| |
TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complements for specified symbols.
| |
TryGetDefaultGapSymbol |
Gets the default Gap symbol.
| |
TryGetDefaultTerminationSymbol |
Gets the default Termination symbol.
| |
TryGetGapSymbols |
Gets the Gap symbol.
| |
TryGetTerminationSymbols |
Gets the Termination symbol.
| |
ValidateSequence |
Validates if all symbols provided are Protein 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.) |