/// <summary>
/// For input sequence, constructs k-mers by sliding
/// a frame of size kmerLength along the input sequence.
/// Track positions of occurance for each kmer in sequence.
/// Constructs KmersOfSequence for sequence and associated k-mers.
/// </summary>
/// <param name="sequence">Input sequence.</param>
/// <param name="kmerLength">K-mer length.</param>
/// <returns>KmersOfSequence constructed from sequence and associated k-mers.</returns>
public static KmerPositionDictionary BuildKmerDictionary(ISequence sequence, int kmerLength)
{
if (sequence == null)
{
throw new ArgumentNullException("sequence");
}
if (kmerLength > sequence.Count)
{
throw new ArgumentException(Properties.Resource.KmerLengthIsTooLong);
}
// kmers maintains the map between k-mer strings to list of positions in sequence.
KmerPositionDictionary kmers = new KmerPositionDictionary();
// Sequence 'kmer' stores the k-mer in each window.
// Construct each k-mer using range from sequence.
for (long i = 0; i <= sequence.Count - kmerLength; ++i)
{
ISequence kmerString = sequence.GetSubSequence(i, kmerLength);
if (kmers.ContainsKey(kmerString))
{
kmers[kmerString].Add(i);
}
else
{
kmers[kmerString] = new List <long>()
{
i
};
}
}
return(kmers);
}
/// <summary>
/// For input sequence, constructs k-mers by sliding
/// a frame of size kmerLength along the input sequence.
/// Track positions of occurance for each kmer in sequence.
/// Constructs KmersOfSequence for sequence and associated k-mers.
/// </summary>
/// <param name="sequence">Input sequence.</param>
/// <param name="kmerLength">K-mer length.</param>
/// <returns>KmersOfSequence constructed from sequence and associated k-mers.</returns>
public static KmerPositionDictionary BuildKmerDictionary(ISequence sequence, int kmerLength)
{
if (sequence == null)
{
throw new ArgumentNullException("sequence");
}
if (kmerLength > sequence.Count)
{
throw new ArgumentException(Properties.Resource.KmerLengthIsTooLong);
}
// kmers maintains the map between k-mer strings to list of positions in sequence.
KmerPositionDictionary kmers = new KmerPositionDictionary();
// Sequence 'kmer' stores the k-mer in each window.
// Construct each k-mer using range from sequence.
for (long i = 0; i <= sequence.Count - kmerLength; ++i)
{
ISequence kmerString = sequence.GetSubSequence(i, kmerLength);
if (kmers.ContainsKey(kmerString))
{
kmers[kmerString].Add(i);
}
else
{
kmers[kmerString] = new List<long>() { i };
}
}
return kmers;
}
