/// <summary>
/// Removes item from the list of aligned sequences in the PairwiseSequenceAlignment.
/// Throws exception if PairwiseSequenceAlignment is read only.
/// </summary>
/// <param name="item">Aligned sequence object</param>
/// <returns>True if item was removed, false if item was not found.</returns>
public bool Remove(PairwiseAlignedSequence item)
{
if (IsReadOnly)
{
Trace.Report(Resource.READ_ONLY_COLLECTION_MESSAGE);
throw new NotSupportedException(Resource.READ_ONLY_COLLECTION_MESSAGE);
}
return(_alignedSequences.Remove(item));
}
/// <summary>
/// Adds an aligned sequence to the list of aligned sequences in the PairwiseSequenceAlignment.
/// Throws exception if sequence alignment is read only.
/// </summary>
/// <param name="item">PairwiseAlignedSequence to add.</param>
public void Add(PairwiseAlignedSequence item)
{
if (IsReadOnly)
{
Trace.Report(Resource.READ_ONLY_COLLECTION_MESSAGE);
throw new NotSupportedException(Resource.READ_ONLY_COLLECTION_MESSAGE);
}
_alignedSequences.Add(item);
}
/// <summary>
/// Convert the delta alignment object to its sequence representation
/// </summary>
/// <returns>Reference sequence alignment at 0th index and
/// Query sequence alignment at 1st index</returns>
internal PairwiseAlignedSequence ConvertDeltaToSequences()
{
PairwiseAlignedSequence alignedSequence = new PairwiseAlignedSequence();
Sequence referenceSequence = null;
Sequence querySequence = null;
int gap = 0;
int length = 0;
List <int> startOffsets = new List <int>(2);
List <int> endOffsets = new List <int>(2);
List <int> insertions = new List <int>(2);
startOffsets.Add(FirstSequenceStart);
startOffsets.Add(SecondSequenceStart);
endOffsets.Add(FirstSequenceEnd);
endOffsets.Add(SecondSequenceEnd);
insertions.Add(0);
insertions.Add(0);
// Create the new sequence object with given start and end indices
referenceSequence = new Sequence(ReferenceSequence.Alphabet);
referenceSequence.IsReadOnly = false;
length = FirstSequenceEnd - FirstSequenceStart + 1;
referenceSequence.InsertRange(
0,
ReferenceSequence.Range(FirstSequenceStart, length).ToString());
querySequence = new Sequence(QuerySequence.Alphabet);
querySequence.IsReadOnly = false;
length = SecondSequenceEnd - SecondSequenceStart + 1;
querySequence.InsertRange(
0,
QuerySequence.Range(SecondSequenceStart, length).ToString());
// Insert the Alignment character at delta position
// +ve delta: Insertion in reference sequence
// -ve delta: Insertion in query sequence (deletion in reference sequence)
foreach (int delta in Deltas)
{
gap += Math.Abs(delta);
if (delta < 0)
{
referenceSequence.Insert(gap - 1, DnaAlphabet.Instance.Gap.Symbol);
insertions[0]++;
}
else
{
querySequence.Insert(gap - 1, DnaAlphabet.Instance.Gap.Symbol);
insertions[1]++;
}
}
alignedSequence.FirstSequence = referenceSequence;
alignedSequence.SecondSequence = querySequence;
alignedSequence.Metadata["StartOffsets"] = startOffsets;
alignedSequence.Metadata["EndOffsets"] = endOffsets;
alignedSequence.Metadata["Insertions"] = insertions;
return(alignedSequence);
}
/// <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);
}
/// <summary>
/// Returns true if the PairwiseSequenceAlignment contains the aligned sequence in the
/// list of aligned sequences.
/// </summary>
/// <param name="item">PairwiseAlignedSequence object</param>
/// <returns>True if contains item, otherwise returns false.</returns>
public bool Contains(PairwiseAlignedSequence item)
{
return(_alignedSequences.Contains(item));
}
