/// <summary>
/// Find the next eligible sequence for alignment/extension
/// </summary>
/// <param name="clusters">List of clusters</param>
/// <param name="currentCluster">Current cluster</param>
/// <param name="targetReference">target position in reference sequence</param>
/// <param name="targetQuery">target position in query sequence</param>
/// <returns>Forward cluster in the list</returns>
private Cluster GetNextCluster(
IList<Cluster> clusters,
Cluster currentCluster,
ref long targetReference,
ref long targetQuery)
{
long firstSequenceStart = currentCluster.Matches.Last().ReferenceSequenceOffset
+ currentCluster.Matches.Last().Length - 1;
long secondSequenceStart = currentCluster.Matches.Last().QuerySequenceOffset
+ currentCluster.Matches.Last().Length - 1;
long distance = (targetReference - firstSequenceStart < targetQuery - secondSequenceStart)
? targetReference - firstSequenceStart
: targetQuery - secondSequenceStart;
Cluster clusterIterator;
Cluster cluster = null;
for (int clusterIndex = clusters.IndexOf(currentCluster) + 1;
clusterIndex < clusters.Count;
clusterIndex++)
{
clusterIterator = clusters[clusterIndex];
if (currentCluster.QueryDirection == clusterIterator.QueryDirection)
{
long firstSequenceEnd = clusterIterator.Matches.First().ReferenceSequenceOffset;
long secondSequenceEnd = clusterIterator.Matches.First().QuerySequenceOffset;
if ((firstSequenceEnd < firstSequenceStart)
&& (clusterIterator.Matches.Last().ReferenceSequenceOffset >= firstSequenceStart)
&& (clusterIterator.Matches.Last().QuerySequenceOffset >= secondSequenceStart))
{
foreach (MatchExtension match in clusterIterator.Matches)
{
if ((firstSequenceEnd < firstSequenceStart)
|| (secondSequenceEnd < secondSequenceStart))
{
firstSequenceEnd = match.ReferenceSequenceOffset;
secondSequenceEnd = match.QuerySequenceOffset;
}
}
}
if ((firstSequenceEnd >= firstSequenceStart)
&& (secondSequenceEnd >= secondSequenceStart))
{
long gapHigh;
long gapLow;
if ((firstSequenceEnd - firstSequenceStart)
> (secondSequenceEnd - secondSequenceStart))
{
gapHigh = firstSequenceEnd - firstSequenceStart;
gapLow = secondSequenceEnd - secondSequenceStart;
}
else
{
gapLow = firstSequenceEnd - firstSequenceStart;
gapHigh = secondSequenceEnd - secondSequenceStart;
}
if (gapHigh < BreakLength
|| ((gapLow * _nucmerAligner.ValidScore) +
((gapHigh - gapLow)
* _nucmerAligner.GapExtensionScore)) >= 0)
{
cluster = clusterIterator;
targetReference = firstSequenceEnd;
targetQuery = secondSequenceEnd;
break;
}
else if ((gapHigh << 1) - gapLow < distance)
{
cluster = clusterIterator;
targetReference = firstSequenceEnd;
targetQuery = secondSequenceEnd;
distance = (gapHigh << 1) - gapLow;
}
}
}
}
return cluster;
}
/// <summary>
/// Check if the cluster is shadowed (contained in alignment)
/// </summary>
/// <param name="alignments">List of alignment</param>
/// <param name="currentCluster">current cluster</param>
/// <param name="currentDeltaAlignment">Current delta alignment</param>
/// <returns>Is cluster contained in alignment</returns>
private static bool IsClusterShadowed(
List<DeltaAlignment> alignments,
Cluster currentCluster,
DeltaAlignment currentDeltaAlignment)
{
DeltaAlignment alignment;
long firstSequenceStart = currentCluster.Matches.First().ReferenceSequenceOffset;
long firstSequenceEnd = currentCluster.Matches.Last().ReferenceSequenceOffset
+ currentCluster.Matches.Last().Length - 1;
long secondSequenceStart = currentCluster.Matches.First().QuerySequenceOffset;
long secondSequenceEnd = currentCluster.Matches.Last().QuerySequenceOffset
+ currentCluster.Matches.Last().Length - 1;
if (0 < alignments.Count)
{
int counter;
for (counter = alignments.IndexOf(currentDeltaAlignment); counter >= 0; counter--)
{
alignment = alignments[counter];
if (alignment.QueryDirection == currentCluster.QueryDirection)
{
if ((alignment.FirstSequenceEnd >= firstSequenceEnd)
&& alignment.SecondSequenceEnd >= secondSequenceEnd
&& alignment.FirstSequenceStart <= firstSequenceStart
&& alignment.SecondSequenceStart <= secondSequenceStart)
{
break;
}
}
}
if (counter >= 0)
{
return true;
}
}
return false;
}
/// <summary>
/// Create a new delta alignment
/// </summary>
/// <param name="referenceSequence">Reference sequence</param>
/// <param name="querySequence">Query sequence</param>
/// <param name="cluster">Cluster object</param>
/// <param name="match">Match object</param>
/// <returns>Newly created DeltaAlignment object</returns>
internal static DeltaAlignment NewAlignment(
ISequence referenceSequence,
ISequence querySequence,
Cluster cluster,
MatchExtension match)
{
DeltaAlignment deltaAlignment = new DeltaAlignment(referenceSequence, querySequence)
{
FirstSequenceStart = match.ReferenceSequenceOffset,
SecondSequenceStart = match.QuerySequenceOffset,
FirstSequenceEnd = match.ReferenceSequenceOffset + match.Length - 1,
SecondSequenceEnd = match.QuerySequenceOffset + match.Length - 1,
QueryDirection = cluster.QueryDirection
};
return deltaAlignment;
}
public void ValidateClusterToString()
{
var match = new Match();
var matchExtn1 = new MatchExtension(match);
matchExtn1.ID = 1;
matchExtn1.Length = 20;
var matchExtn2 = new MatchExtension(match);
matchExtn2.ID = 2;
matchExtn2.Length = 30;
IList<MatchExtension> extnList = new List<MatchExtension>();
extnList.Add(matchExtn1);
extnList.Add(matchExtn2);
var clust = new Cluster(extnList);
string actualString = clust.ToString();
string expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.ClusterExpectedNode);
Assert.AreEqual(actualString, expectedString.Replace("\\r\\n", System.Environment.NewLine));
}
public void TestClusterToString()
{
Match match = new Match();
MatchExtension matchExtn1 = new MatchExtension(match);
matchExtn1.ID = 1;
matchExtn1.Length = 20;
MatchExtension matchExtn2 = new MatchExtension(match);
matchExtn2.ID = 2;
matchExtn2.Length = 30;
IList<MatchExtension> extnList = new List<MatchExtension>();
extnList.Add(matchExtn1);
extnList.Add(matchExtn2);
Cluster clust = new Cluster(extnList);
string actualString = clust.ToString();
string expectedString = "RefStart=0 QueryStart=0 Length=20 Score=0 WrapScore=0 IsGood=False\r\nRefStart=0 QueryStart=0 Length=30 Score=0 WrapScore=0 IsGood=False\r\n".Replace ("\r\n", Environment.NewLine);
Assert.AreEqual(actualString, expectedString);
}
