/// <summary>
/// Creates triplet groups of nucleobases along the specified range. the
/// range must be of appropriate length, i.e. a multiple of the codon length.
/// </summary>
/// <param name="seq">RNA sequence to group</param>
/// <param name="startIndex">index of the first nucleobase in the first codon</param>
/// <param name="stopIndex">index of the first nucleobase in the last codon</param>
/// <returns>Returns list of AACodons</returns>
private List <AACodon> CreateReadingFrame(Nucleobase[] seq, int startIndex, int stopIndex)
{
if (stopIndex < startIndex + this.codonLength)
{
throw new ArgumentException("stop index must be at least " + this.codonLength +
"greater than start index.");
}
int rangeLength = stopIndex - startIndex;
if (rangeLength % 3 != 0)
{
throw new ArgumentException("the length of the reading frame must"
+ "be a multiple of " + this.codonLength + " -- in other words, " +
"the reading frame must contain a whole number of codons.");
}
List <AACodon> triplets = new List <AACodon>();
int lengthDiff = seq.Length - this.codonLength; //readability
for (int i = startIndex; i < stopIndex + this.codonLength; i += this.codonLength)
{
triplets.Add(AACodonExtension.BuildAACodon(seq, i, i + this.codonLength));
}
return(triplets);
}
/// <summary>
/// Scans the given sequence for a codon in the provided list, returning the
/// index of the first base in the found codon
/// </summary>
/// <param name="seq">sequence to scan</param>
/// <param name="cod">set of codons to scan for</param>
/// <param name="beginScan">index at which to begin scanning for the specified codon</param>
/// <returns>Returns the index of the first nucleobase in a matching sequence</returns>
private int Scan(Nucleobase[] seq, List <AACodon> cod, int beginScan, int granularity)
{
if (this.codonLength >= seq.Length - beginScan)
{
throw new ArgumentException("given codon is longer than the provided sequence");
}
else if (beginScan < 0 || beginScan > seq.Length)
{
throw new ArgumentOutOfRangeException("scan must begin at a valid index. Attempted scan start: " +
beginScan + ". Sequence length: " + seq.Length + ".");
}
for (int i = beginScan; i < seq.Length - this.codonLength + 1; i += granularity)
{
var tempCodon = AACodonExtension.BuildAACodon(seq, i, i + this.codonLength);
if (cod.Contains(tempCodon))
{
return(i);
}
}
throw new CodonNotFoundException();
}