/// <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>
/// Builds k-mers from a list of given input sequences.
/// For each sequence in input list, constructs a KmersOfSequence
/// corresponding to the sequence and associated k-mers.
/// </summary>
/// <param name="sequences">List of input sequences.</param>
/// <param name="kmerLength">K-mer length.</param>
/// <returns>List of KmersOfSequence instances.</returns>
public static KmerIndexerDictionary BuildKmerDictionary(IList <ISequence> sequences, int kmerLength)
{
if (sequences == null)
{
throw new ArgumentNullException("sequences");
}
if (kmerLength <= 0)
{
throw new ArgumentException(Properties.Resource.KmerLengthShouldBePositive);
}
Task <KmerPositionDictionary>[] kmerTasks = new Task <KmerPositionDictionary> [sequences.Count];
for (int index = 0; index < sequences.Count; index++)
{
ISequence localSequence = sequences[index];
kmerTasks[index] = Task <KmerPositionDictionary> .Factory.StartNew(
o => BuildKmerDictionary(localSequence, kmerLength), TaskCreationOptions.None);
}
IList <KmerIndexer> kmerIndex;
List <KmerPositionDictionary> kmerPositionDictionaries = new List <KmerPositionDictionary>(kmerTasks.Length);
int totalElements = 0;
for (int index = 0; index < kmerTasks.Length; index++)
{
KmerPositionDictionary kmerPositionDictionary = kmerTasks[index].Result;
kmerPositionDictionaries.Add(kmerPositionDictionary);
totalElements += kmerPositionDictionary.Count;
}
KmerIndexerDictionary maps = new KmerIndexerDictionary(totalElements);
for (int index = 0; index < kmerPositionDictionaries.Count; index++)
{
foreach (KeyValuePair <ISequence, IList <long> > value in kmerPositionDictionaries[index])
{
if (maps.TryGetValue(value.Key, out kmerIndex) ||
maps.TryGetValue(value.Key.GetReverseComplementedSequence(), out kmerIndex))
{
kmerIndex.Add(new KmerIndexer(index, value.Value));
}
else
{
maps.Add(value.Key, new List <KmerIndexer> {
new KmerIndexer(index, value.Value)
});
}
}
}
return(maps);
}
/// <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;
}
