/// <summary>
/// Analyze the passed contig and store a consensus into its Consensus property.
/// </summary>
/// <param name="contig">Contig for which consensus is to be constructed</param>
private void MakeConsensus(Contig contig)
{
List <byte> positionItems = new List <byte>(), consensusSequence = new List <byte>();
// there's no simple way to pre-guess the length of the contig
long position = 0;
while (true)
{
// Initialization
positionItems.Clear();
// Add the sequences
positionItems.AddRange(from aseq in contig.Sequences
where position >= aseq.Position && position < aseq.Position + aseq.Sequence.Count
let seqPos = aseq.IsReversed ? (aseq.Sequence.Count() - 1) - (position - aseq.Position) : position - aseq.Position
select aseq.IsComplemented ? aseq.Sequence.GetComplementedSequence()[seqPos] : aseq.Sequence[seqPos]);
if (positionItems.Count == 0)
{
// This means no sequences at this position. We're done
contig.Consensus = new Sequence(Alphabets.AmbiguousAlphabetMap[_sequenceAlphabet], consensusSequence.ToArray());
return;
}
consensusSequence.Add(ConsensusResolver.GetConsensus(positionItems.ToArray()));
position++;
}
}
/// <summary>
/// Analyze the given sequences and store a consensus into its Consensus property.
/// </summary>
/// <param name="referenceSequence">Reference sequence.</param>
/// <param name="querySequence">Query sequence.</param>
/// <returns>Consensus of sequences.</returns>
protected ISequence MakeConsensus(
ISequence referenceSequence,
ISequence querySequence)
{
if (referenceSequence == null)
{
throw new ArgumentNullException("referenceSequence");
}
if (querySequence == null)
{
throw new ArgumentNullException("querySequence");
}
// For each pair of symbols (characters) in reference and query sequence
// get the consensus symbol and append it.
byte[] consensus = new byte[referenceSequence.Count];
for (int index = 0; index < referenceSequence.Count; index++)
{
consensus[index] = ConsensusResolver.GetConsensus(
new byte[] { referenceSequence[index], querySequence[index] });
}
IAlphabet alphabet = Alphabets.AutoDetectAlphabet(consensus, 0, consensus.LongLength, referenceSequence.Alphabet);
return(new Sequence(alphabet, consensus, false));
}
/// <summary>
/// Analyze the passed contig and store a consensus into its Consensus property.
/// </summary>
/// <param name="contig">Contig for which consensus is to be constructed</param>
private void MakeConsensus(Contig contig)
{
List <byte> positionItems = new List <byte>();
List <byte> consensusSequence = new List <byte>();
// there's no simple way to pre-guess the length of the contig
long position = 0;
while (true)
{
// Initializations
positionItems.Clear();
foreach (Contig.AssembledSequence aseq in contig.Sequences)
{
if (position >= aseq.Position && position < aseq.Position + aseq.Sequence.Count)
{
long seqPos;
if (aseq.IsReversed)
{
seqPos = (aseq.Sequence.Count() - 1) - (position - aseq.Position);
}
else
{
seqPos = position - aseq.Position;
}
if (aseq.IsComplemented)
{
positionItems.Add(aseq.Sequence.GetComplementedSequence()[seqPos]);
}
else
{
positionItems.Add(aseq.Sequence[seqPos]);
}
}
}
if (positionItems.Count == 0)
{
// This means no sequences at this position. We're done
contig.Consensus = new Sequence(Alphabets.AmbiguousAlphabetMap[_sequenceAlphabet], consensusSequence.ToArray());
return;
}
else
{
consensusSequence.Add(ConsensusResolver.GetConsensus(positionItems.ToArray()));
}
position++;
}
}
/// <summary>
/// Analyze the passed contig and store a consensus into its Consensus property.
/// </summary>
/// <param name="contig">Contig for which consensus is to be constructed</param>
private void MakeConsensus(Contig contig)
{
Sequence consensusSequence = new Sequence(_sequenceAlphabet);
List <ISequenceItem> positionItems = new List <ISequenceItem>();
// there's no simple way to pre-guess the length of the contig
int position = 0;
while (true)
{
// Initializations
positionItems.Clear();
foreach (Contig.AssembledSequence aseq in contig.Sequences)
{
if (position >= aseq.Position && position < aseq.Position + aseq.Sequence.Count)
{
int seqPos;
if (aseq.IsReversed)
{
seqPos = (aseq.Sequence.Count - 1) - (position - aseq.Position);
}
else
{
seqPos = position - aseq.Position;
}
if (aseq.IsComplemented)
{
positionItems.Add(aseq.Sequence.Complement[seqPos]);
}
else
{
positionItems.Add(aseq.Sequence[seqPos]);
}
}
}
if (positionItems.Count == 0)
{
// This means no sequences at this position. We're done
contig.Consensus = consensusSequence;
return;
}
else
{
consensusSequence.Add(ConsensusResolver.GetConsensus(positionItems));
}
position++;
}
}
/// <summary>
/// Adds consensus to the alignment result. At this point, it is a very simple algorithm
/// which puts an ambiguity character where the two aligned sequences do not match.
/// Uses X and N for protein and DNA/RNA alignments, respectively.
/// </summary>
/// <param name="alignment">
/// Alignment to which to add the consensus. This is the result returned by the main Align
/// or AlignSimple method, which contains the aligned sequences but not yet a consensus sequence.
/// </param>
private void AddSimpleConsensusToResult(PairwiseAlignedSequence alignment)
{
ISequence seq0 = alignment.FirstSequence;
ISequence seq1 = alignment.SecondSequence;
byte[] consensus = new byte[seq0.Count];
for (int i = 0; i < seq0.Count; i++)
{
consensus[i] = ConsensusResolver.GetConsensus(
new byte[] { seq0[i], seq1[i] });
}
IAlphabet consensusAlphabet = Alphabets.AutoDetectAlphabet(consensus, 0, consensus.GetLongLength(), seq0.Alphabet);
alignment.Consensus = new Sequence(consensusAlphabet, consensus, false);
}
/// <summary>
/// Adds consensus to the alignment result. At this point, it is a very simple algorithm
/// which puts an ambiguity character where the two aligned sequences do not match.
/// Uses X and N for protein and DNA/RNA alignments, respectively.
/// </summary>
/// <param name="alignment">
/// Alignment to which to add the consensus. This is the result returned by the main Align
/// or AlignSimple method, which contains the aligned sequences but not yet a consensus sequence.
/// </param>
private void AddSimpleConsensusToResult(PairwiseAlignedSequence alignment)
{
ISequence seq0 = alignment.FirstSequence;
ISequence seq1 = alignment.SecondSequence;
Sequence consensus = new Sequence(seq0.Alphabet);
for (int i = 0; i < seq0.Count; i++)
{
consensus.Add(
ConsensusResolver.GetConsensus(
new List <ISequenceItem>()
{
seq0[i], seq1[i]
}));
}
alignment.Consensus = consensus;
}
/// <summary>
/// Analyze the given seqquences and store a consensus into its Consensus property.
/// </summary>
/// <param name="referenceSequence">Reference sequence</param>
/// <param name="querySequence">Query sequence</param>
/// <returns>Consensus of sequences</returns>
protected override ISequence MakeConsensus(
ISequence referenceSequence,
ISequence querySequence)
{
// For each pair of symbols (characters) in reference and query sequence
// get the consensus symbol and append it.
Sequence consensus = new Sequence(referenceSequence.Alphabet);
for (int index = 0; index < referenceSequence.Count; index++)
{
consensus.Add(
ConsensusResolver.GetConsensus(
new List <ISequenceItem>()
{
referenceSequence[index], querySequence[index]
}));
}
return(consensus);
}
