/// <summary>
/// Extracts joined subsequence without complement flag.
/// </summary>
/// <param name="sourceSequence">
/// The complete sequence.
/// </param>
/// <param name="subsequence">
/// The subsequence.
/// </param>
/// <returns>
/// The <see cref="Chain"/>.
/// </returns>
private Chain ExtractJoinedSubsequenceWithoutComplement(Sequence sourceSequence, Subsequence subsequence)
{
var joinedSequence = sourceSequence.GetSubSequence(subsequence.Start, subsequence.Length).ConvertToString();
var position = subsequence.Position.ToArray();
for (int j = 0; j < position.Length; j++)
{
joinedSequence += sourceSequence.GetSubSequence(position[j].Start, position[j].Length).ConvertToString();
}
return new Chain(joinedSequence);
}
/// <summary>
/// Extracts subsequence without joins (additional positions).
/// </summary>
/// <param name="sourceSequence">
/// The complete sequence.
/// </param>
/// <param name="subsequence">
/// The subsequence.
/// </param>
/// <returns>
/// The <see cref="Chain"/>.
/// </returns>
private Chain ExtractSimpleSubsequence(Sequence sourceSequence, Subsequence subsequence)
{
ISequence bioSequence = sourceSequence.GetSubSequence(subsequence.Start, subsequence.Length);
if (subsequence.SequenceAttribute.Any(sa => sa.Attribute == LibiadaWeb.Attribute.Complement))
{
bioSequence = bioSequence.GetReverseComplementedSequence();
}
return new Chain(bioSequence.ConvertToString());
}
/// <summary>
/// Extracts joined subsequence with complement flag.
/// </summary>
/// <param name="sourceSequence">
/// The complete sequence.
/// </param>
/// <param name="subsequence">
/// The subsequence.
/// </param>
/// <returns>
/// The <see cref="Chain"/>.
/// </returns>
private Chain ExtractJoinedSubsequenceWithComplement(Sequence sourceSequence, Subsequence subsequence)
{
var bioSequence = sourceSequence.GetSubSequence(subsequence.Start, subsequence.Length);
var position = subsequence.Position.ToArray();
string resultSequence;
if (subsequence.SequenceAttribute.Any(sa => sa.Attribute == Attribute.ComplementJoin))
{
var joinedSequence = bioSequence.ConvertToString();
for (int j = 0; j < position.Length; j++)
{
joinedSequence += sourceSequence.GetSubSequence(position[j].Start, position[j].Length).ConvertToString();
}
resultSequence = new Sequence(Alphabets.DNA, joinedSequence).GetReverseComplementedSequence().ConvertToString();
}
else
{
resultSequence = bioSequence.GetReverseComplementedSequence().ConvertToString();
for (int j = 0; j < position.Length; j++)
{
resultSequence += sourceSequence.GetSubSequence(position[j].Start, position[j].Length).GetReverseComplementedSequence().ConvertToString();
}
}
return new Chain(resultSequence);
}
