Calculate redundancy of a genetic code using Comeron's counting scheme.
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#include <Sequence/RedundancyCom95.hpp>
List of all members.
Public Member Functions |
| | RedundancyCom95 (const Sequence::GeneticCodes &genetic_code=Sequence::UNIVERSAL) |
| double | FirstNon (const std::string &codon) const throw (Sequence::SeqException) |
| double | First2S (const std::string &codon) const throw (Sequence::SeqException) |
| double | First2V (const std::string &codon) const throw (Sequence::SeqException) |
| double | ThirdNon (const std::string &codon) const throw (Sequence::SeqException) |
| double | ThirdFour (const std::string &codon) const throw (Sequence::SeqException) |
| double | Third2S (const std::string &codon) const throw (Sequence::SeqException) |
| double | Third2V (const std::string &codon) const throw (Sequence::SeqException) |
| double | L0_vals (const std::string &codon) const throw (Sequence::SeqException) |
| double | L2S_vals (const std::string &codon) const throw (Sequence::SeqException) |
| double | L2V_vals (const std::string &codon) const throw (Sequence::SeqException) |
| double | L4_vals (const std::string &codon) const throw (Sequence::SeqException) |
Detailed Description
Calculate redundancy of a genetic code using Comeron's counting scheme.
This class performs "on-the-fly" tabulations of the redundancy of a genetic code, in terms of whether or not a transition or transversion at any site in the codon changes the amino acid encoded by that codon. It supports whatever codes libsequence supports, because it uses Sequence::Translate to determine whether a mutation at a certain position in a codon will encode the same amino acid or not.
This should be considered a "buried" class, in the sense that it is, properly speaking, an implementation detail specific to Sequence::Comeron95. Another possible use for this class (which I will implement), is for analysis of silent/replacement polymorphism in population-genetic data.
- Note:
- any variable of type std::string that is named codon implicity assumes codon.length()==3
Definition at line 57 of file RedundancyCom95.hpp.
Constructor & Destructor Documentation
| Sequence::RedundancyCom95::RedundancyCom95 |
( |
const Sequence::GeneticCodes & |
genetic_code = Sequence::UNIVERSAL |
) |
[explicit] |
Member Function Documentation
- Returns:
- number of times the first codon position is synonymous via a transition
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
Definition at line 449 of file RedundancyCom95.cc.
- Returns:
- number of times the first codon position is synonymous via a transversion
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
Definition at line 462 of file RedundancyCom95.cc.
- Returns:
- number of times the first codon position is non-degenerate
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
Definition at line 437 of file RedundancyCom95.cc.
- Returns:
- the number of non-degenerate positions in codon
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
- Note:
- the return value = 1.0+FirstNon(codon )+ThirdNon(codon)
Definition at line 523 of file RedundancyCom95.cc.
- Returns:
- the number of transitional silent sites in codon
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
- Note:
- the return value = First2S(codon )+Third2S(codon )
Definition at line 536 of file RedundancyCom95.cc.
- Returns:
- the number of transversional silent sites in codon
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
- Note:
- the return value = First2V(codon )+Third2V(codon )
Definition at line 549 of file RedundancyCom95.cc.
- Returns:
- the number of fourfold silent sites in codon
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
- Note:
- the return value = ThirdFour(codon )
Definition at line 562 of file RedundancyCom95.cc.
- Returns:
- number of times the third position is synonymous via a transition
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
Definition at line 499 of file RedundancyCom95.cc.
- Returns:
- number of times the third position is synonymous via a transversion
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
Definition at line 511 of file RedundancyCom95.cc.
| double Sequence::RedundancyCom95::ThirdFour |
( |
const std::string & |
codon |
) |
const throw (Sequence::SeqException) |
- Returns:
- number of times the third position is fourfold-degenerate
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
Definition at line 487 of file RedundancyCom95.cc.
- Returns:
- number of times the third position is non-degenerate
- Precondition:
- codon is of length 3, is all uppercase, and only contains the characters {A,G,C,T}
- Exceptions:
-
Definition at line 475 of file RedundancyCom95.cc.
The documentation for this class was generated from the following files:
