/// <summary>
/// Gets the sequence from the specified node.
/// </summary>
/// <param name="node">DeBruijn node.</param>
/// <returns>Returns an instance of sequence.</returns>
public ISequence GetNodeSequence(DeBruijnNode node)
{
if (node == null)
{
throw new ArgumentNullException("node");
}
return(new Sequence(Alphabets.DNA, node.GetOriginalSymbols(this.KmerLength)));
}
/// <summary>
/// Gets the last or first symbol in the node depending on the isForwardDirection flag is true or false.
/// If the isSameOrientation flag is false then symbol will be taken from the ReverseComplement of the kmer data.
/// </summary>
/// <param name="node">DeBruijn node.</param>
/// <param name="isForwardDirection">Flag to indicate whether the node is in forward direction or not.</param>
/// <param name="isSameOrientation">Flag to indicate the orientation.</param>
/// <returns>Byte represnting the symbol.</returns>
public byte GetNextSymbolFrom(DeBruijnNode node, bool isForwardDirection, bool isSameOrientation)
{
if (node == null)
{
throw new ArgumentNullException("node");
}
byte[] nextSequence = isSameOrientation
? node.GetOriginalSymbols(KmerLength)
: node.GetReverseComplementOfOriginalSymbols(KmerLength);
return(isForwardDirection ? nextSequence.Last() : nextSequence.First());
}
/// <summary>
/// This gets the next symbol from a node while forming chains. This can be made a lot more efficient if it turns in to a bottleneck.
/// all chains are extended from either the first or last base present in the node, and this base is either forward
/// or reverse complimented, this method reflects this.
/// </summary>
/// <param name="node">Next node</param>
/// <param name="graph">Graph to get symbol from</param>
/// <param name="GetFirstNotLast">First or last base?</param>
/// <param name="ReverseComplimentBase">Should the compliment of the base be returned</param>
/// <returns></returns>
private static byte GetNextSymbol(DeBruijnNode node, int kmerLength, bool GetRCofFirstBaseInsteadOfLastBase)
{
if (node == null)
{
throw new ArgumentNullException("node");
}
byte[] symbols = node.GetOriginalSymbols(kmerLength);
byte value = GetRCofFirstBaseInsteadOfLastBase ? symbols.First() : symbols.Last();
if (GetRCofFirstBaseInsteadOfLastBase)
{
byte value2;
bool rced = DnaAlphabet.Instance.TryGetComplementSymbol(value, out value2);
//Should never happend
if (!rced)
{
throw new Exception("Could not revcomp base during graph construction");
}
value = value2;
}
return(value);
}
/// <summary>
/// Gets the last or first symbol in the node depending on the isForwardDirection flag is true or false.
/// If the isSameOrientation flag is false then symbol will be taken from the ReverseComplement of the kmer data.
/// </summary>
/// <param name="node">DeBruijn node.</param>
/// <param name="isForwardDirection">Flag to indicate whether the node is in forward direction or not.</param>
/// <param name="isSameOrientation">Flag to indicate the orientation.</param>
/// <returns>Byte represnting the symbol.</returns>
public byte GetNextSymbolFrom(DeBruijnNode node, bool isForwardDirection, bool isSameOrientation)
{
if (node == null)
throw new ArgumentNullException("node");
byte[] nextSequence = isSameOrientation
? node.GetOriginalSymbols(KmerLength)
: node.GetReverseComplementOfOriginalSymbols(KmerLength);
return isForwardDirection
? nextSequence.Last()
: nextSequence.First();
}
/// <summary>
/// Gets the sequence from the specified node.
/// </summary>
/// <param name="node">DeBruijn node.</param>
/// <returns>Returns an instance of sequence.</returns>
public ISequence GetNodeSequence(DeBruijnNode node)
{
if (node == null)
{
throw new ArgumentNullException("node");
}
return new Sequence(Alphabets.DNA, node.GetOriginalSymbols(KmerLength));
}
