/// <summary>
/// Align the Gap by executing pairwise alignment
/// </summary>
/// <param name="referenceSequence">Reference sequence</param>
/// <param name="querySequence">Query Sequence</param>
/// <param name="sequenceResult1">Editable sequence containing alignment first result</param>
/// <param name="sequenceResult2">Editable sequence containing alignment second result</param>
/// <param name="consensusResult">Editable sequence containing consensus sequence</param>
/// <param name="mum1">First MUM of Gap</param>
/// <param name="mum2">Second MUM of Gap</param>
/// <param name="insertions">Insetions made to the aligned sequences.</param>
/// <returns>Score of alignment</returns>
private int AlignGap(
ISequence referenceSequence,
ISequence querySequence,
ISequence sequenceResult1,
ISequence sequenceResult2,
ISequence consensusResult,
MaxUniqueMatch mum1,
MaxUniqueMatch mum2,
out List <int> insertions)
{
int score = 0;
ISequence sequence1 = null;
ISequence sequence2 = null;
IList <IPairwiseSequenceAlignment> sequenceAlignment = null;
string mum1String = string.Empty;
string mum2String = string.Empty;
insertions = new List <int>(2);
insertions.Add(0);
insertions.Add(0);
int mum1ReferenceStartIndex = 0;
int mum1QueryStartIndex = 0;
int mum1Length = 0;
int mum2ReferenceStartIndex = 0;
int mum2QueryStartIndex = 0;
int mum2Length = 0;
if (null != mum1)
{
mum1ReferenceStartIndex = mum1.FirstSequenceStart;
mum1QueryStartIndex = mum1.SecondSequenceStart;
mum1Length = mum1.Length;
}
if (null != mum2)
{
mum2ReferenceStartIndex = mum2.FirstSequenceStart;
mum2QueryStartIndex = mum2.SecondSequenceStart;
mum2Length = mum2.Length;
}
else
{
mum2ReferenceStartIndex = referenceSequence.Count;
mum2QueryStartIndex = querySequence.Count;
}
int referenceGapStartIndex = mum1ReferenceStartIndex + mum1Length;
int queryGapStartIndex = mum1QueryStartIndex + mum1Length;
if (mum2ReferenceStartIndex > referenceGapStartIndex &&
mum2QueryStartIndex > queryGapStartIndex)
{
sequence1 = referenceSequence.Range(
referenceGapStartIndex,
mum2ReferenceStartIndex - referenceGapStartIndex);
sequence2 = querySequence.Range(
queryGapStartIndex,
mum2QueryStartIndex - queryGapStartIndex);
sequenceAlignment = RunPairWise(sequence1, sequence2);
if (sequenceAlignment != null)
{
foreach (IPairwiseSequenceAlignment pairwiseAlignment in sequenceAlignment)
{
foreach (PairwiseAlignedSequence alignment in pairwiseAlignment.PairwiseAlignedSequences)
{
sequenceResult1.InsertRange(
sequenceResult1.Count,
alignment.FirstSequence.ToString());
sequenceResult2.InsertRange(
sequenceResult2.Count,
alignment.SecondSequence.ToString());
consensusResult.InsertRange(
consensusResult.Count,
alignment.Consensus.ToString());
score += alignment.Score;
if (alignment.Metadata.ContainsKey("Insertions"))
{
List <int> gapinsertions = alignment.Metadata["Insertions"] as List <int>;
if (gapinsertions != null)
{
if (gapinsertions.Count > 0)
{
insertions[0] += gapinsertions[0];
}
if (gapinsertions.Count > 1)
{
insertions[1] += gapinsertions[1];
}
}
}
}
}
}
}
else if (mum2ReferenceStartIndex > referenceGapStartIndex)
{
sequence1 = referenceSequence.Range(
referenceGapStartIndex,
mum2ReferenceStartIndex - referenceGapStartIndex);
sequenceResult1.InsertRange(sequenceResult1.Count, sequence1.ToString());
sequenceResult2.InsertRange(sequenceResult2.Count, CreateDefaultGap(sequence1.Count));
consensusResult.InsertRange(consensusResult.Count, sequence1.ToString());
insertions[1] += sequence1.Count;
if (UseGapExtensionCost)
{
score = GapOpenCost + ((sequence1.Count - 1) * GapExtensionCost);
}
else
{
score = sequence1.Count * GapOpenCost;
}
}
else if (mum2QueryStartIndex > queryGapStartIndex)
{
sequence2 = querySequence.Range(
queryGapStartIndex,
mum2QueryStartIndex - queryGapStartIndex);
sequenceResult1.InsertRange(sequenceResult1.Count, CreateDefaultGap(sequence2.Count));
sequenceResult2.InsertRange(sequenceResult2.Count, sequence2.ToString());
consensusResult.InsertRange(consensusResult.Count, sequence2.ToString());
insertions[0] += sequence2.Count;
if (UseGapExtensionCost)
{
score = GapOpenCost + ((sequence2.Count - 1) * GapExtensionCost);
}
else
{
score = sequence2.Count * GapOpenCost;
}
}
// Add the MUM to the result
if (0 < mum2Length)
{
mum1String = referenceSequence.Range(
mum2ReferenceStartIndex,
mum2Length).ToString();
sequenceResult1.InsertRange(sequenceResult1.Count, mum1String);
mum2String = querySequence.Range(
mum2QueryStartIndex,
mum2Length).ToString();
sequenceResult2.InsertRange(sequenceResult2.Count, mum2String);
consensusResult.InsertRange(consensusResult.Count, mum1String);
// Get the byte array (indices of symbol in MUM)
byte[] indices = SimilarityMatrix.ToByteArray(mum1String);
// Calculate the score
foreach (byte index in indices)
{
score += SimilarityMatrix[index, index];
}
}
return(score);
}
/// <summary>
/// get all the gaps in each sequence and call pairwise alignment
/// </summary>
/// <param name="referenceSequence">Reference sequence</param>
/// <param name="sequence">Query sequence</param>
/// <returns>Aligned sequences</returns>
private PairwiseAlignedSequence ProcessGaps(
ISequence referenceSequence,
ISequence sequence)
{
Sequence sequenceResult1;
Sequence sequenceResult2;
Sequence consensusResult;
MaxUniqueMatch mum1 = null;
MaxUniqueMatch mum2 = null;
PairwiseAlignedSequence alignedSequence = new PairwiseAlignedSequence();
sequenceResult1 = new Sequence(referenceSequence.Alphabet);
sequenceResult1.IsReadOnly = false;
sequenceResult1.ID = referenceSequence.ID;
sequenceResult1.DisplayID = referenceSequence.DisplayID;
sequenceResult2 = new Sequence(referenceSequence.Alphabet);
sequenceResult2.IsReadOnly = false;
sequenceResult2.ID = sequence.ID;
sequenceResult2.DisplayID = sequence.DisplayID;
consensusResult = new Sequence(referenceSequence.Alphabet);
consensusResult.IsReadOnly = false;
consensusResult.ID = sequence.ID;
consensusResult.DisplayID = sequence.DisplayID;
// Run the alignment for gap before first MUM
List <int> insertions = new List <int>(2);
insertions.Add(0);
insertions.Add(0);
List <int> gapInsertions;
mum1 = _finalMumList[0];
alignedSequence.Score += AlignGap(
referenceSequence,
sequence,
sequenceResult1,
sequenceResult2,
consensusResult,
null, // Here the first MUM does not exist
mum1,
out gapInsertions);
insertions[0] += gapInsertions[0];
insertions[1] += gapInsertions[1];
// Run the alignment for all the gaps between MUM
for (int index = 1; index < _finalMumList.Count; index++)
{
mum2 = _finalMumList[index];
alignedSequence.Score += AlignGap(
referenceSequence,
sequence,
sequenceResult1,
sequenceResult2,
consensusResult,
mum1,
mum2,
out gapInsertions);
insertions[0] += gapInsertions[0];
insertions[1] += gapInsertions[1];
mum1 = mum2;
}
// Run the alignment for gap after last MUM
alignedSequence.Score += AlignGap(
referenceSequence,
sequence,
sequenceResult1,
sequenceResult2,
consensusResult,
mum1,
null,
out gapInsertions);
insertions[0] += gapInsertions[0];
insertions[1] += gapInsertions[1];
alignedSequence.FirstSequence = sequenceResult1;
alignedSequence.SecondSequence = sequenceResult2;
alignedSequence.Consensus = consensusResult;
// Offset is not required as Smith Waterman will fragmented alignment.
// Offset is the starting position of alignment of sequence1 with respect to sequence2.
if (PairWiseAlgorithm is NeedlemanWunschAligner)
{
alignedSequence.FirstOffset = sequenceResult1.IndexOfNonGap() - referenceSequence.IndexOfNonGap();
alignedSequence.SecondOffset = sequenceResult2.IndexOfNonGap() - sequence.IndexOfNonGap();
}
List <int> startOffsets = new List <int>(2);
List <int> endOffsets = new List <int>(2);
startOffsets.Add(0);
startOffsets.Add(0);
endOffsets.Add(referenceSequence.Count - 1);
endOffsets.Add(sequence.Count - 1);
alignedSequence.Metadata["StartOffsets"] = startOffsets;
alignedSequence.Metadata["EndOffsets"] = endOffsets;
alignedSequence.Metadata["Insertions"] = insertions;
// return the aligned sequence
return(alignedSequence);
}