/// <summary>
/// Basic constructor for an amino acid.
/// </summary>
/// <param name="src">Codon used to generate this amino acid</param>
/// <param name="i">Index of this AA in the protein sequence</param>
/// <param name="name">Full name of the AA</param>
/// <param name="abb">Abbreviated name</param>
/// <param name="s">Shorthand symbol</param>
public AminoAcid(AACodon src, String name, String abb, Char s)
{
this.source = src;
this.symbol = s;
this.fullName = name;
this.abbrev = abb;
}
/// <summary>
/// Constructor for Ribosome instances.
/// </summary>
/// <param name="startCodon">The codon accepted as the start codon.</param>
/// <param name="stopCodons">Set of codons accepted as the stop codon.</param>
/// <param name="factory">Rules for generating AminoAcids from codons</param>
/// <param name="codonLength">length of an invidual codon; should be consistent
/// with start/stop codons</param>
public Ribosome(AACodon startCodon, List <AACodon> stopCodons, IAAFactory factory, int codonLength)
{
this.startCodon = startCodon;
this.stopCodons = stopCodons;
this.factory = factory;
this.codonLength = codonLength;
}
//initializes the 'default' ribosome to be used in testing
// might have to change based on actual syntax
public void Init()
{
start = AACodon.AUG;
stops = new List <AACodon>
{
AACodon.UGA,
AACodon.UAA,
AACodon.UAG
};
seq = FrameshiftUtil.StringSeq("AUGCCCUAA");
r = new Ribosome(start, stops, new AAFactory(), 3);
}
/// <summary>
/// Given an amino acid codon, returns a sequence of
/// nucleobases corresponding to that codon
/// </summary>
/// <param name="codon">Codon to break down</param>
/// <returns>Array of appropriate bases</returns>
public static Nucleobase[] BreakAACodon(AACodon codon)
{
return(FrameshiftUtil.StringSeq(codon.ToString())); //TODO
}
/// <summary>
/// Overload for scan, used when there's only a single possible codon to scan for.
/// uses the default granularity of 1
/// </summary>
private int Scan(Nucleobase[] seq, AACodon cod, int beginScan)
{
return(Scan(seq, new List <AACodon> {
cod
}, beginScan, 1));
}
public IAminoAcid BuildAA(AACodon codon)
{
switch (codon)
{
case AACodon.UUU:
case AACodon.UUC:
//phenylalanine
return(new AminoAcid(codon, "Phenylalanine", "Phe", 'F'));
case AACodon.UUA:
case AACodon.UUG:
case AACodon.CUU:
case AACodon.CUC:
case AACodon.CUA:
case AACodon.CUG:
//leucine
return(new AminoAcid(codon, "Leucine", "Leu", 'L'));
case AACodon.UCU:
case AACodon.UCC:
case AACodon.UCA:
case AACodon.UCG:
case AACodon.AGU:
case AACodon.AGC:
//serine
return(new AminoAcid(codon, "Serine", "Ser", 'S'));
case AACodon.UAU:
case AACodon.UAC:
//tyrosine;
return(new AminoAcid(codon, "Tyrosine", "Tyr", 'T'));
case AACodon.UGU:
case AACodon.UGC:
//cysteine
return(new AminoAcid(codon, "Cysteine", "Cys", 'C'));
case AACodon.UGG:
//tryptophan;
return(new AminoAcid(codon, "Tryptophan", "Trp", 'W'));
case AACodon.CCU:
case AACodon.CCC:
case AACodon.CCA:
case AACodon.CCG:
//proline
return(new AminoAcid(codon, "Proline", "Pro", 'P'));
case AACodon.CAU:
case AACodon.CAC:
//histidine
return(new AminoAcid(codon, "Histidine", "His", 'H'));
case AACodon.CAA:
case AACodon.CAG:
//glutamine
return(new AminoAcid(codon, "Glutamine", "Gln", 'Q'));
case AACodon.CGU:
case AACodon.CGC:
case AACodon.CGA:
case AACodon.CGG:
case AACodon.AGA:
case AACodon.AGG:
//arginine
return(new AminoAcid(codon, "Arginine", "Arg", 'R'));
case AACodon.AUU:
case AACodon.AUC:
case AACodon.AUA:
//isoleucine
return(new AminoAcid(codon, "Isoleucine", "Ile", 'I'));
case AACodon.AUG:
//met / start
return(new AminoAcid(codon, "Methionine", "Met", 'M'));
case AACodon.ACU:
case AACodon.ACC:
case AACodon.ACA:
case AACodon.ACG:
//threonine
return(new AminoAcid(codon, "Threonine", "Thr", 'T'));
case AACodon.AAU:
case AACodon.AAC:
//asparagine
return(new AminoAcid(codon, "Asparagine", "Asn", 'N'));
case AACodon.AAA:
case AACodon.AAG:
//lycine
return(new AminoAcid(codon, "Lycine", "Lys", 'K'));
case AACodon.GUU:
case AACodon.GUC:
case AACodon.GUA:
case AACodon.GUG:
//valine
return(new AminoAcid(codon, "Valine", "Val", 'V'));
case AACodon.GCU:
case AACodon.GCC:
case AACodon.GCA:
case AACodon.GCG:
//alanine
return(new AminoAcid(codon, "Alanine", "Ala", 'A'));
case AACodon.GAU:
case AACodon.GAC:
//aspartic acid
return(new AminoAcid(codon, "Apartic Acid", "Asp", 'D'));
case AACodon.GAA:
case AACodon.GAG:
//glutamic acid
return(new AminoAcid(codon, "Glutamic Acid", "Glu", 'E'));
case AACodon.GGU:
case AACodon.GGC:
case AACodon.GGA:
case AACodon.GGG:
//glycine;
return(new AminoAcid(codon, "Glycine", "Gly", 'G'));
case AACodon.UAA:
case AACodon.UAG:
case AACodon.UGA:
//stop
return(new AminoAcid(codon, "STOP", "END", '_'));
default: return(null);
}
}
