Function to build the elements aaList, geneticCode, peptideList, used by function getConstraint.

Description

To be run before the first use of function getConstraint. This function generates the variables aaList, geneticCode and peptideList, a list of all the peptides (up to length 5), used by function getConstraint.

Usage

1

Value

aaList

Vector of all amino acids.

geneticCode

A list describing the standard genetic code.

peptideList

A list of all the peptides (up to length 5).

Author(s)

Sophie Lebre <sophie.lebre@umontpellier.fr>

References

Lebre and Gascuel, The combinatorics of overlapping genes (freely available from arXiv at:

http://arxiv.org/abs/1602.04971).

See Also

getConstraint

Examples

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	## Not run: 
# 1) Build peptideList, used by function getConstraint.
mydata <- build_data()
aaList <- mydata$aaList
geneticCode <- mydata$geneticCode
peptideList <- mydata$peptideList

# 2) Ask for the constraint induced on a chosen peptide in a chosen overlapping frame

## amino acid contraints 
getConstraint("C", frame = -2, code=geneticCode, pepList=peptideList) 
getConstraint("D", frame = 1, code=geneticCode, pepList=peptideList)

## 3-peptide contraints
getConstraint("CWC",frame = -2, code=geneticCode, pepList=peptideList)

## 5-peptide contraints
getConstraint("CWCCC",frame = -2, code=geneticCode, pepList=peptideList)
	
## End(Not run)