/// <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="start">Start index of sequence range.</param>
/// <param name="end">End index of sequence range.</param>
/// <param name="kmerLength">Kmer Length.</param>
/// <param name="sequences">List of sequences.</param>
/// <returns>Kmer Dictionary.</returns>
public static Dictionary <string, KmerDataGraphNodePair> BuildPaDeNAKmerDictionary(
int start,
int end,
int kmerLength,
IList <ISequence> sequences)
{
if (kmerLength <= 0)
{
throw new ArgumentException(Resource.KmerLengthShouldBePositive);
}
if (sequences == null)
{
throw new ArgumentNullException("sequences");
}
char[] rcBuilder = new char[kmerLength];
Dictionary <string, KmerDataGraphNodePair> kmerDict = new Dictionary <string, KmerDataGraphNodePair>();
for (int index = start; index < end; index++)
{
// Sequence 'kmer' stores the k-mer in each window.
// Construct each k-mer using range from sequence
for (int i = 0; i <= sequences[index].Count - kmerLength; ++i)
{
ISequence kmerSeq = sequences[index].Range(i, kmerLength);
if (!kmerSeq.Any <ISequenceItem>(a => a.IsAmbiguous || a.IsGap))
{
string kmerString = kmerSeq.ToString();
string kmerStringRC = kmerString.GetReverseComplement(rcBuilder);
bool isNormalOrientation = string.Compare(kmerString, kmerStringRC, StringComparison.OrdinalIgnoreCase) <= 0;
string kmer = isNormalOrientation ? kmerString : kmerStringRC; //take the alphabetically first one
KmerDataGraphNodePair kmerData;
if (!kmerDict.TryGetValue(kmer, out kmerData))
{
kmerDict.Add(kmer,
new KmerDataGraphNodePair(new KmerData(index, i, isNormalOrientation), isNormalOrientation));
}
else
{
kmerData.Kmer.IncrementCount(isNormalOrientation);
}
}
}
}
return(kmerDict);
}
public static ISequence <bool> All <T>(this ISequence <T> source, Func <T, bool> predicate)
{
return(source.Any(x => !predicate(x)).Select(x => !x));
}
public static ISequence <bool> Any <T>(this ISequence <T> source)
{
return(source.Any(x => true));
}