/// <summary>
/// get the clusters
/// </summary>
/// <param name="matchExtensionList">List of Matches of a read.</param>
/// <param name="sortedMatches">Flag to indicate that the matches are sorted or not.</param>
/// <returns>List of clusters</returns>
public IList <Cluster> GetClusters(List <MatchExtension> matchExtensionList, bool sortedMatches)
{
ClusterBuilder clusterBuilder = new ClusterBuilder();
if (-1 < FixedSeparation)
{
clusterBuilder.FixedSeparation = FixedSeparation;
}
if (-1 < MaximumSeparation)
{
clusterBuilder.MaximumSeparation = MaximumSeparation;
}
if (-1 < MinimumScore)
{
clusterBuilder.MinimumScore = MinimumScore;
}
if (-1 < SeparationFactor)
{
clusterBuilder.SeparationFactor = SeparationFactor;
}
clusterBuilder.ScoreMethod = ScoreMethod;
return(clusterBuilder.BuildClusters(matchExtensionList, sortedMatches));
}
/// <summary>
/// get the clusters
/// </summary>
/// <param name="mumList">List of maximum unique matches</param>
/// <returns>List of clusters</returns>
protected override IList <Cluster> GetClusters(
IList <MaxUniqueMatch> mumList)
{
IClusterBuilder clusterBuilder = new ClusterBuilder();
if (-1 < FixedSeparation)
{
clusterBuilder.FixedSeparation = FixedSeparation;
}
if (-1 < MaximumSeparation)
{
clusterBuilder.MaximumSeparation = MaximumSeparation;
}
if (-1 < MinimumScore)
{
clusterBuilder.MinimumScore = MinimumScore;
}
if (-1 < SeparationFactor)
{
clusterBuilder.SeparationFactor = SeparationFactor;
}
return(clusterBuilder.BuildClusters(mumList));
}
/// <summary>
/// get the clusters
/// </summary>
/// <param name="mumList">List of maximum unique matches</param>
/// <returns>List of clusters</returns>
private IList <Cluster> GetClusters(
IList <MatchExtension> mumList)
{
IClusterBuilder clusterBuilder = new ClusterBuilder();
if (-1 < FixedSeparation)
{
clusterBuilder.FixedSeparation = FixedSeparation;
}
if (-1 < MaximumSeparation)
{
clusterBuilder.MaximumSeparation = MaximumSeparation;
}
if (-1 < MinimumScore)
{
clusterBuilder.MinimumScore = MinimumScore;
}
if (-1 < SeparationFactor)
{
clusterBuilder.SeparationFactor = SeparationFactor;
}
return(clusterBuilder.BuildClusters(mumList));
}
/// <summary>
/// get the clusters
/// </summary>
/// <param name="matchExtensionList">List of Matches of a read.</param>
/// <param name="sortedMatches">Flag to indicate that the matches are sorted or not.</param>
/// <returns>List of clusters</returns>
public IList<Cluster> GetClusters(List<MatchExtension> matchExtensionList, bool sortedMatches)
{
ClusterBuilder clusterBuilder = new ClusterBuilder();
if (-1 < FixedSeparation)
{
clusterBuilder.FixedSeparation = FixedSeparation;
}
if (-1 < MaximumSeparation)
{
clusterBuilder.MaximumSeparation = MaximumSeparation;
}
if (-1 < MinimumScore)
{
clusterBuilder.MinimumScore = MinimumScore;
}
if (-1 < SeparationFactor)
{
clusterBuilder.SeparationFactor = SeparationFactor;
}
clusterBuilder.ScoreMethod = ScoreMethod;
return clusterBuilder.BuildClusters(matchExtensionList, sortedMatches);
}
/// <summary>
/// Validates the Cluster Builder Matches for the input provided.
/// </summary>
/// <param name="matches">Max Unique Match list</param>
/// <param name="nodeName">Node name to be read from xml</param>
/// <param name="propParam">Property parameters</param>
/// <returns>True, if successfully validated</returns>
private bool ValidateClusterBuilderMatches(IEnumerable<Match> matches, string nodeName, PropertyParameters propParam)
{
// Validates the Cluster builder MUMs
string firstSeqOrderExpected = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustFirstSequenceMumOrderNode);
string lengthExpected = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustLengthNode);
string secondSeqOrderExpected = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustSecondSequenceMumOrderNode);
var firstSeqOrderActual = new StringBuilder();
var lengthActual = new StringBuilder();
var secondSeqOrderActual = new StringBuilder();
var cbObj = new ClusterBuilder {MinimumScore = 0};
switch (propParam)
{
case PropertyParameters.MinimumScore:
cbObj.MinimumScore = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MinimumScoreNode), null);
break;
case PropertyParameters.MaximumSeparation:
cbObj.MaximumSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MaximumSeparationNode), null);
break;
case PropertyParameters.FixedSeparation:
cbObj.FixedSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
case PropertyParameters.SeparationFactor:
cbObj.SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
break;
case PropertyParameters.FixedSeparationAndSeparationFactor:
cbObj.SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
cbObj.FixedSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
case PropertyParameters.MaximumFixedAndSeparationFactor:
cbObj.MaximumSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MaximumSeparationNode), null);
cbObj.SeparationFactor = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeparationFactorNode), null);
cbObj.FixedSeparation = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FixedSeparationNode), null);
break;
default:
break;
}
var meObj = matches.Select(m => new MatchExtension(m)).ToList();
IEnumerable<Cluster> clusts = cbObj.BuildClusters(meObj);
foreach (MatchExtension maxMatchExtension in clusts.SelectMany(clust => clust.Matches))
{
firstSeqOrderActual.Append(maxMatchExtension.ReferenceSequenceOffset);
secondSeqOrderActual.Append(maxMatchExtension.QuerySequenceOffset);
lengthActual.Append(maxMatchExtension.Length);
}
if ((0 != string.Compare(firstSeqOrderExpected.Replace(",", ""), firstSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(lengthExpected.Replace(",", ""), lengthActual.ToString(), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(secondSeqOrderExpected.Replace(",", ""), secondSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture)))
{
ApplicationLog.WriteLine("NUCmer P1 : Cluster builder match not matching");
return false;
}
return true;
}
/// <summary>
/// Validates the Unique Matches for the input provided.
/// </summary>
/// <param name="matches">Max Unique Match list</param>
/// <param name="nodeName">Node name to be read from xml</param>
/// <param name="additionalParam">Unique Match/Sub level LIS/LIS</param>
/// <param name="isFilePath">Nodes to be read from Text file?</param>
/// <returns>True, if successfully validated</returns>
bool ValidateUniqueMatches(IList<Match> matches,
string nodeName, AdditionalParameters additionalParam, bool isFilePath)
{
switch (additionalParam)
{
case AdditionalParameters.PerformClusterBuilder:
// Validates the Cluster builder MUMs
string firstSeqOrderExpected =
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustFirstSequenceStartNode);
string lengthExpected =
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustLengthNode);
string secondSeqOrderExpected =
this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustSecondSequenceStartNode);
StringBuilder firstSeqOrderActual = new StringBuilder();
StringBuilder lengthActual = new StringBuilder();
StringBuilder secondSeqOrderActual = new StringBuilder();
ClusterBuilder cb = new ClusterBuilder { MinimumScore = 0 };
List<MatchExtension> meObj = matches.Select(m => new MatchExtension(m)).ToList();
// Order the mum list with query sequence order and
// Assign query sequence to the MUM's
for (int index = 0; index < meObj.Count(); index++)
{
meObj.ElementAt(index).ReferenceSequenceMumOrder = index + 1;
meObj.ElementAt(index).QuerySequenceMumOrder = index + 1;
}
List<Cluster> clusts = cb.BuildClusters(meObj);
foreach (Cluster clust in clusts)
{
foreach (MatchExtension maxMatchExtension in clust.Matches)
{
firstSeqOrderActual.Append(maxMatchExtension.ReferenceSequenceMumOrder);
secondSeqOrderActual.Append(maxMatchExtension.QuerySequenceMumOrder);
lengthActual.Append(maxMatchExtension.Length);
}
}
if ((0 != string.Compare(firstSeqOrderExpected.Replace(",", ""),
firstSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(lengthExpected.Replace(",", ""),
lengthActual.ToString(), true, CultureInfo.CurrentCulture))
|| (0 != string.Compare(secondSeqOrderExpected.Replace(",", ""),
secondSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture)))
{
ApplicationLog.WriteLine("NUCmer BVT : Unique match not matching");
return false;
}
break;
case AdditionalParameters.FindUniqueMatches:
// Gets all the unique matches properties to be validated as in xml.
string[] firstSeqOrder = null;
string[] length = null;
string[] secondSeqOrder = null;
if (isFilePath)
{
firstSeqOrder = this.utilityObj.xmlUtil.GetFileTextValue(nodeName,
Constants.FirstSequenceMumOrderNode).Split(',');
length = this.utilityObj.xmlUtil.GetFileTextValue(nodeName,
Constants.LengthNode).Split(',');
secondSeqOrder = this.utilityObj.xmlUtil.GetFileTextValue(nodeName,
Constants.SecondSequenceMumOrderNode).Split(',');
}
else
{
firstSeqOrder = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FirstSequenceMumOrderNode).Split(',');
length = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LengthNode).Split(',');
secondSeqOrder = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SecondSequenceMumOrderNode).Split(',');
}
int i = 0;
IList<MatchExtension> meNewObj = matches.Select(m => new MatchExtension(m)).ToList();
// Order the mum list with query sequence order and
// Assign query sequence to the MUM's
for (int index = 0; index < meNewObj.Count(); index++)
{
meNewObj.ElementAt(index).ReferenceSequenceMumOrder = index + 1;
meNewObj.ElementAt(index).QuerySequenceMumOrder = index + 1;
}
// Loops through all the matches and validates the same.
foreach (MatchExtension match in meNewObj)
{
if ((0 != string.Compare(firstSeqOrder[i],
match.ReferenceSequenceMumOrder.ToString((IFormatProvider)null), true,
CultureInfo.CurrentCulture))
|| (0 != string.Compare(length[i],
match.Length.ToString((IFormatProvider)null), true,
CultureInfo.CurrentCulture))
|| (0 != string.Compare(secondSeqOrder[i],
match.QuerySequenceMumOrder.ToString((IFormatProvider)null), true,
CultureInfo.CurrentCulture)))
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Unique match not matching at index '{0}'", i.ToString((IFormatProvider)null)));
return false;
}
i++;
}
break;
default:
break;
}
return true;
}