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Alphabets used in Seq objects etc to declare sequence type and letters.
This is used by sequences which contain a finite number of similar words.
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Alphabet | |||
SingleLetterAlphabet | |||
ProteinAlphabet | |||
NucleotideAlphabet | |||
DNAAlphabet | |||
RNAAlphabet | |||
SecondaryStructure | |||
ThreeLetterProtein | |||
AlphabetEncoder | |||
Gapped | |||
HasStopCodon |
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Returns a common but often generic base alphabet object (PRIVATE). This throws away any AlphabetEncoder information, e.g. Gapped alphabets. Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single letter. These DO NOT raise an exception! |
Returns a common but often generic alphabet object (PRIVATE). Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single letter. These DO NOT raise an exception! This is aware of Gapped and HasStopCodon and new letters added by other AlphabetEncoders. This WILL raise an exception if more than one gap character or stop symbol is present. |
Returns True except for DNA+RNA or Nucleotide+Protein (PRIVATE). This relies on the Alphabet subclassing hierarchy. It does not check things like gap characters or stop symbols. |
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