/// <summary>
/// Constructs a Mismatcher object to compare against a refreence sequence.
/// </summary>
/// <param name="referenceSequence">The sequence against which query sequences will be compared,</param>
public Mismatcher(ISequence referenceSequence)
{
if (referenceSequence == null)
{
throw new ArgumentNullException("referenceSequence");
}
this.mummer = new MUMmer.MUMmer(referenceSequence);
this.ReferenceSequence = referenceSequence;
}
/// <summary>
///
/// </summary>
/// <param name="suffixTree"></param>
public NUCmer(ISuffixTree suffixTree)
{
if (suffixTree == null)
{
throw new ArgumentNullException("suffixTree");
}
// Mummer with the reference sequence.
_internalMummer = new MUMmer.MUMmer(suffixTree);
_internalReferenceSequence = _internalMummer.ReferenceSequence;
SetDefaults();
}
/// <summary>
/// Initializes a new instance of the NUCmer class.
/// </summary>
public NUCmer(ISequence referenceSequence)
{
if (referenceSequence == null)
{
throw new ArgumentNullException("referenceSequence");
}
// Mummer with the reference sequence.
_internalMummer = new MUMmer.MUMmer(referenceSequence);
_internalReferenceSequence = referenceSequence;
SetDefaults();
}
/// <summary>
///
/// </summary>
/// <param name="suffixTree"></param>
public NUCmer(ISuffixTree suffixTree)
{
if (suffixTree == null)
{
throw new ArgumentNullException("suffixTree");
}
// Mummer with the reference sequence.
_internalMummer = new MUMmer.MUMmer(suffixTree);
_internalReferenceSequence = _internalMummer.ReferenceSequence;
SetDefaults();
}
/// <summary>
/// Initializes a new instance of the NUCmer class.
/// </summary>
public NUCmer(ISequence referenceSequence)
{
if (referenceSequence == null)
{
throw new ArgumentNullException("referenceSequence");
}
// Mummer with the reference sequence.
_internalMummer = new MUMmer.MUMmer(referenceSequence);
_internalReferenceSequence = referenceSequence;
SetDefaults();
}
/// <summary>
/// Generates Delta Alignments.
/// </summary>
/// <param name="referenceSequences">Enumerable of Reference Sequences.</param>
/// <param name="querySequences">Enumerable of Query Sequences.</param>
/// <param name="isUniqueInReference">Whether MUMs are unique in query or not.</param>
/// <returns>List of enumerable of delta alignments.</returns>
public List <IEnumerable <DeltaAlignment> > GetDeltaAlignments(
IEnumerable <ISequence> referenceSequences,
IEnumerable <ISequence> querySequences,
bool isUniqueInReference = true)
{
internalReferenceSequence = referenceSequences.ElementAt(0);
List <IEnumerable <DeltaAlignment> > result = new List <IEnumerable <DeltaAlignment> >();
if (1 > LengthOfMUM)
{
string message = Properties.Resource.MUMLengthTooSmall;
Trace.Report(message);
throw new ArgumentException(message);
}
// Step:1 concat all the sequences into one sequence
if (referenceSequences.Count() > 1)
{
internalReferenceSequence = ConcatSequence(referenceSequences);
}
Sequence seq = internalReferenceSequence as Sequence;
if (seq == null)
{
throw new ArgumentException(Properties.Resource.OnlySequenceClassSupported);
}
long referenceSequenceCount = seq.Count;
// Mummer for performaing step 3
MUMmer.MUMmer internalMummer = new MUMmer.MUMmer(seq)
{
LengthOfMUM = LengthOfMUM
};
foreach (ISequence sequence in querySequences)
{
if (sequence.Equals(internalReferenceSequence))
{
continue;
}
// Step3 : streaming process is performed with the query sequence
IEnumerable <Match> matches;
if (isUniqueInReference)
{
matches = internalMummer.GetMatchesUniqueInReference(sequence);
}
else
{
matches = internalMummer.GetMatches(sequence);
}
// Convert matches to matchextensions
internalMumList = new List <MatchExtension>();
long mumOrder = 1;
foreach (Match currentMatch in matches)
{
internalMumList.Add(new MatchExtension(currentMatch)
{
ReferenceSequenceMumOrder = mumOrder,
QuerySequenceMumOrder = mumOrder,
Query = sequence
});
}
if (internalMumList.Count > 0)
{
// Step 5 : Get the list of Clusters
internalClusterList = GetClusters(internalMumList);
// Step 7: Process Clusters and get delta
result.Add(ProcessCluster(
referenceSequences,
internalClusterList, referenceSequenceCount));
}
}
return(result);
}