| MummerProteinAlphabet Class |
Alphabet for use by MUMmer to support concatenation character '+'
Inheritance HierarchySystemObject
BioProteinAlphabet
BioAmbiguousProteinAlphabet
Bio.Algorithms.MUMmerMummerProteinAlphabet
BioProteinAlphabet
BioAmbiguousProteinAlphabet
Bio.Algorithms.MUMmerMummerProteinAlphabet
Namespace: Bio.Algorithms.MUMmer
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe MummerProteinAlphabet type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | MummerProteinAlphabet |
Initializes a new instance of the AmbiguousDnaAlphabet class.
|
Properties| Name | Description | |
|---|---|---|
 | A |
Gets the Alanine Amino acid.
(Inherited from ProteinAlphabet.) |
| B |
Gets the Aspartic Acid or Asparagine.
(Inherited from AmbiguousProteinAlphabet.) |
| C |
Gets the Cysteine Amino acid.
(Inherited from ProteinAlphabet.) |
| ConcatenationChar |
Gets the Concatenation character
|
| Count |
Gets count of nucleotides.
(Inherited from ProteinAlphabet.) |
| D |
Gets the Aspartic Acid.
(Inherited from ProteinAlphabet.) |
| E |
Gets the Glutamic Acid.
(Inherited from ProteinAlphabet.) |
| F |
Gets the Phenylalanine Amino acid.
(Inherited from ProteinAlphabet.) |
| G |
Gets the Glycine Amino acid.
(Inherited from ProteinAlphabet.) |
| Gap |
Gets the Gap character.
(Inherited from ProteinAlphabet.) |
| H |
Gets the Histidine Amino acid.
(Inherited from ProteinAlphabet.) |
| HasAmbiguity |
Gets or sets a value indicating whether this alphabet has ambiguous characters.
This alphabet does have ambiguous characters.
(Inherited from ProteinAlphabet.) |
| HasGaps |
Gets or sets a value indicating whether this alphabet has a gap character.
This alphabet does have a gap character.
(Inherited from ProteinAlphabet.) |
| HasTerminations |
Gets or sets a value indicating whether this alphabet has termination characters.
This alphabet does have termination characters.
(Inherited from ProteinAlphabet.) |
| I |
Gets the Isoleucine Amino acid.
(Inherited from ProteinAlphabet.) |
| IsComplementSupported |
Gets or sets a value indicating whether complement is supported or not.
(Inherited from ProteinAlphabet.) |
| Item |
Gets the byte value of item at the given index.
(Inherited from ProteinAlphabet.) |
| J |
Gets the Leucine or Isoleucine.
(Inherited from AmbiguousProteinAlphabet.) |
| K |
Gets the Lysine Amino acid.
(Inherited from ProteinAlphabet.) |
| L |
Gets the Leucine Amino acid.
(Inherited from ProteinAlphabet.) |
| M |
Gets the Methionine Amino acid.
(Inherited from ProteinAlphabet.) |
| N |
Gets the Asparagine Amino acid.
(Inherited from ProteinAlphabet.) |
| Name |
Gets or sets the name of this alphabet - this is always 'Protein'.
(Inherited from ProteinAlphabet.) |
| O |
Gets the Pyrrolysine Amino acid.
(Inherited from ProteinAlphabet.) |
| P |
Gets the Proline Amino acid.
(Inherited from ProteinAlphabet.) |
| Q |
Gets the Glutamine Amino acid.
(Inherited from ProteinAlphabet.) |
| R |
Gets the Arginine Amino acid.
(Inherited from ProteinAlphabet.) |
| S |
Gets the Serine Amino acid.
(Inherited from ProteinAlphabet.) |
| T |
Gets the Threoine Amino acid.
(Inherited from ProteinAlphabet.) |
| Ter |
Gets the Termination character.
(Inherited from ProteinAlphabet.) |
| U |
Gets the Selenocysteine Amino acid.
(Inherited from ProteinAlphabet.) |
| V |
Gets the Valine Amino acid.
(Inherited from ProteinAlphabet.) |
| W |
Gets the Tryptophan Amino acid.
(Inherited from ProteinAlphabet.) |
| X |
Gets X - Xxx - Undetermined or atypical.
(Inherited from AmbiguousProteinAlphabet.) |
| Y |
Gets the Tyrosine Amino acid.
(Inherited from ProteinAlphabet.) |
| Z |
Gets Z - Glx - Glutamic Acid or Glutamine.
(Inherited from AmbiguousProteinAlphabet.) |
Methods| Name | Description | |
|---|---|---|
| AddAminoAcid |
Adds a Amino acid to the existing amino acids.
(Inherited from ProteinAlphabet.) |
 | CheckIsAmbiguous |
Checks if the provided item is an ambiguous character or not
(Inherited from ProteinAlphabet.) |
| CheckIsGap |
Checks if the provided item is a gap character or not
(Inherited from ProteinAlphabet.) |
| CompareSymbols |
Compares two symbols.
(Inherited from ProteinAlphabet.) |
| 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.
(Inherited from ProteinAlphabet.) |
| GetConsensusSymbol |
Find the consensus nucleotide for a set of nucleotides.
(Inherited from AmbiguousProteinAlphabet.) |
| GetEnumerator |
Byte array of nucleotides.
(Inherited from ProteinAlphabet.) |
| GetFriendlyName |
Gets the friendly name of a given symbol.
(Inherited from ProteinAlphabet.) |
| 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 ProteinAlphabet.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| GetValidSymbols |
Gets the valid symbol.
(Inherited from ProteinAlphabet.) |
| 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.
(Inherited from ProteinAlphabet.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ToString |
Converts the Protein Alphabets to string.
(Inherited from ProteinAlphabet.) |
| TryGetAmbiguousSymbol |
Gets the Ambiguous symbol.
(Inherited from ProteinAlphabet.) |
| TryGetBasicSymbols |
Gets the Basic symbol.
(Inherited from ProteinAlphabet.) |
| TryGetComplementSymbol(Byte, Byte) |
Gets the complement of the symbol.
(Inherited from ProteinAlphabet.) |
| TryGetComplementSymbol(Byte, Byte) |
This method tries to get the complements for specified symbols.
(Inherited from ProteinAlphabet.) |
| TryGetDefaultGapSymbol |
Gets the default Gap symbol.
(Inherited from ProteinAlphabet.) |
| TryGetDefaultTerminationSymbol |
Gets the default Termination symbol.
(Inherited from ProteinAlphabet.) |
| TryGetGapSymbols |
Gets the Gap symbol.
(Inherited from ProteinAlphabet.) |
| TryGetTerminationSymbols |
Gets the Termination symbol.
(Inherited from ProteinAlphabet.) |
| ValidateSequence |
Validates if all symbols provided are Protein symbols or not.
(Inherited from ProteinAlphabet.) |
Fields
See Also