/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Drived class flows the defined flow by this
/// method. Store generated MUMs in properties MUMs, SortedMUMs.
/// Alignment first finds MUMs for all the query sequence, and then
/// runs pairwise algorithm on gaps to produce alignments.
/// </summary>
/// <param name="referenceSequence">reference sequence</param>
/// <param name="querySequenceList">list of input sequences</param>
/// <returns>A list of sequence alignments</returns>
private IList <IPairwiseSequenceAlignment> AlignmentWithAccumulatedMUMs(
ISequence referenceSequence,
IList <ISequence> querySequenceList)
{
// Get MUMs
_mums = new Dictionary <ISequence, IList <MaxUniqueMatch> >();
_finalMums = new Dictionary <ISequence, IList <MaxUniqueMatch> >();
if (Validate(referenceSequence, querySequenceList))
{
IList <MaxUniqueMatch> mumList;
// Step1 : building suffix trees using reference sequence
ISuffixTree suffixTree = BuildSuffixTree(referenceSequence);
// On each query sequence aligned with reference sequence
foreach (ISequence sequence in querySequenceList)
{
if (sequence.Equals(referenceSequence))
{
continue;
}
// Step2 : streaming process is performed with the query sequence
mumList = Streaming(suffixTree, referenceSequence, sequence, LengthOfMUM);
_mums.Add(sequence, mumList);
// Step3(a) : sorted mum list based on reference sequence
mumList = SortMum(mumList);
if (mumList.Count > 0)
{
// Step3(b) : LIS using greedy cover algorithm
mumList = CollectLongestIncreasingSubsequence(mumList);
}
else
{
mumList = null;
}
_finalMums.Add(sequence, mumList);
}
}
IList <IPairwiseSequenceAlignment> results = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment alignment = null;
if (MUMs != null && FinalMUMs != null)
{
// Getting refernce sequence
_referenceSequence = referenceSequence;
// On each query sequence aligned with reference sequence
foreach (var finalMum in FinalMUMs)
{
var sequence = finalMum.Key;
_mumList = MUMs[sequence];
_finalMumList = finalMum.Value;
alignment = new PairwiseSequenceAlignment(referenceSequence, sequence);
if (_mumList.Count > 0)
{
if (_finalMumList.Count > 0)
{
// Step 4 : get all the gaps in each sequence and call
// pairwise alignment
alignment.PairwiseAlignedSequences.Add(ProcessGaps(referenceSequence, sequence));
}
results.Add(alignment);
}
else
{
IList <IPairwiseSequenceAlignment> sequenceAlignment = RunPairWise(
referenceSequence,
sequence);
foreach (IPairwiseSequenceAlignment pairwiseAlignment in sequenceAlignment)
{
results.Add(pairwiseAlignment);
}
}
}
}
return(results);
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Drived class flows the defined flow by this
/// method.
/// </summary>
/// <param name="referenceSequenceList">reference sequence</param>
/// <param name="querySequenceList">list of input sequences</param>
/// <returns>A list of sequence alignment</returns>
private IList <IPairwiseSequenceAlignment> Alignment(
IList <ISequence> referenceSequenceList,
IList <ISequence> querySequenceList)
{
// Initializations
if (referenceSequenceList.Count > 0)
{
if (ConsensusResolver == null)
{
ConsensusResolver = new SimpleConsensusResolver(referenceSequenceList[0].Alphabet);
}
else
{
ConsensusResolver.SequenceAlphabet = referenceSequenceList[0].Alphabet;
}
}
IList <IPairwiseSequenceAlignment> results = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment sequenceAlignment = null;
IList <DeltaAlignment> deltaAlignments = null;
IList <PairwiseAlignedSequence> alignments = null;
ISequence referenceSequence = null;
// Validate the input
Validate(referenceSequenceList, querySequenceList);
// Step:1 concat all the sequences into one sequence
if (referenceSequenceList.Count > 1)
{
referenceSequence = ConcatSequence(referenceSequenceList);
}
else
{
referenceSequence = referenceSequenceList[0];
}
// Getting refernce sequence
_referenceSequence = referenceSequence;
// Step2 : building suffix trees using reference sequence
_suffixTree = BuildSuffixTree(_referenceSequence);
// On each query sequence aligned with reference sequence
foreach (ISequence sequence in querySequenceList)
{
if (sequence.Equals(referenceSequence))
{
continue;
}
sequenceAlignment = new PairwiseSequenceAlignment(referenceSequence, sequence);
// Step3 : streaming process is performed with the query sequence
_mumList = Streaming(_suffixTree, sequence, LengthOfMUM);
if (_mumList.Count > 0)
{
// Step 5 : Get the list of Clusters
_clusterList = GetClusters(_mumList);
// Step 7: Process Clusters and get delta
deltaAlignments = ProcessCluster(
referenceSequenceList,
_clusterList);
// Step 8: Convert delta alignments to sequence alignments
alignments = ConvertDeltaToAlignment(deltaAlignments);
if (alignments.Count > 0)
{
foreach (PairwiseAlignedSequence align in alignments)
{
// Calculate the score of alignment
align.Score = CalculateScore(
align.FirstSequence,
align.SecondSequence);
// Make Consensus
align.Consensus = MakeConsensus(
align.FirstSequence,
align.SecondSequence);
sequenceAlignment.PairwiseAlignedSequences.Add(align);
}
}
}
results.Add(sequenceAlignment);
}
return(results);
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Drived class flows the defined flow by this
/// method. Does not store MUMs, processes MUMs and gaps to find
/// alignment directly.
/// </summary>
/// <param name="referenceSequence">reference sequence</param>
/// <param name="querySequenceList">list of input sequences</param>
/// <returns>A list of sequence alignments</returns>
private IList <IPairwiseSequenceAlignment> AlignmentWithoutAccumulatedMUMs(
ISequence referenceSequence,
IList <ISequence> querySequenceList)
{
IList <IPairwiseSequenceAlignment> results = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment alignment = null;
if (Validate(referenceSequence, querySequenceList))
{
// Safety check for public methods to ensure that null
// inputs are handled.
if (referenceSequence == null || querySequenceList == null)
{
return(null);
}
// Getting refernce sequence
_referenceSequence = referenceSequence;
// Step1 : building suffix trees using reference sequence
_suffixTree = BuildSuffixTree(_referenceSequence);
// On each query sequence aligned with reference sequence
foreach (ISequence sequence in querySequenceList)
{
if (sequence.Equals(referenceSequence))
{
continue;
}
alignment = new PairwiseSequenceAlignment(referenceSequence, sequence);
// Step2 : streaming process is performed with the query sequence
_mumList = Streaming(_suffixTree, referenceSequence, sequence, LengthOfMUM);
// Step3(a) : sorted mum list based on reference sequence
_sortedMumList = SortMum(_mumList);
if (_sortedMumList.Count > 0)
{
// Step3(b) : LIS using greedy cover algorithm
_finalMumList = CollectLongestIncreasingSubsequence(_sortedMumList);
if (_finalMumList.Count > 0)
{
// Step 4 : get all the gaps in each sequence and call
// pairwise alignment
alignment.PairwiseAlignedSequences.Add(ProcessGaps(referenceSequence, sequence));
}
results.Add(alignment);
}
else
{
IList <IPairwiseSequenceAlignment> sequenceAlignment = RunPairWise(
referenceSequence,
sequence);
foreach (IPairwiseSequenceAlignment pairwiseAlignment in sequenceAlignment)
{
results.Add(pairwiseAlignment);
}
}
}
}
return(results);
}
