public void TestClusterWithCross()
{
// Create a list of Mum classes.
List <MaxUniqueMatch> matches = new List <MaxUniqueMatch>();
MaxUniqueMatch match = null;
match = new MaxUniqueMatch();
match.FirstSequenceStart = 0;
match.Length = 4;
match.SecondSequenceStart = 4;
matches.Add(match);
match = new MaxUniqueMatch();
match.FirstSequenceStart = 4;
match.Length = 3;
match.SecondSequenceStart = 0;
matches.Add(match);
match = new MaxUniqueMatch();
match.FirstSequenceStart = 10;
match.Length = 3;
match.SecondSequenceStart = 10;
matches.Add(match);
IClusterBuilder clusterBuilder = new ClusterBuilder();
clusterBuilder.MinimumScore = 2;
clusterBuilder.FixedSeparation = 0;
IList <Cluster> actualOutput = clusterBuilder.BuildClusters(matches);
IList <Cluster> expectedOutput = new List <Cluster>();
IList <MaxUniqueMatchExtension> clusterMatches = new List <MaxUniqueMatchExtension>();
match = new MaxUniqueMatch();
match.FirstSequenceStart = 0;
match.Length = 4;
match.SecondSequenceStart = 4;
clusterMatches.Add(new MaxUniqueMatchExtension(match));
expectedOutput.Add(new Cluster(clusterMatches));
clusterMatches = new List <MaxUniqueMatchExtension>();
match = new MaxUniqueMatch();
match.FirstSequenceStart = 4;
match.Length = 3;
match.SecondSequenceStart = 0;
clusterMatches.Add(new MaxUniqueMatchExtension(match));
expectedOutput.Add(new Cluster(clusterMatches));
clusterMatches = new List <MaxUniqueMatchExtension>();
match = new MaxUniqueMatch();
match.FirstSequenceStart = 10;
match.Length = 3;
match.SecondSequenceStart = 10;
clusterMatches.Add(new MaxUniqueMatchExtension(match));
expectedOutput.Add(new Cluster(clusterMatches));
Assert.IsTrue(this.CompareMumList(actualOutput, expectedOutput));
}
bool ValidateUniqueMatches(IList <Match> matches,
string nodeName, AdditionalParameters additionalParam, bool isFilePath)
{
switch (additionalParam)
{
case AdditionalParameters.PerformClusterBuilder:
// Validates the Cluster builder MUMs
string firstSeqOrderExpected =
utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustFirstSequenceStartNode);
string lengthExpected =
utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustLengthNode);
string secondSeqOrderExpected =
utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClustSecondSequenceStartNode);
StringBuilder firstSeqOrderActual = new StringBuilder();
StringBuilder lengthActual = new StringBuilder();
StringBuilder secondSeqOrderActual = new StringBuilder();
ClusterBuilder cb = new ClusterBuilder();
cb.MinimumScore = 0;
List <MatchExtension> meObj = new List <MatchExtension>();
foreach (Match m in matches)
{
meObj.Add(new MatchExtension(m));
}
// 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)))
{
Console.WriteLine("NUCmer BVT : Unique match not matching");
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 = utilityObj.xmlUtil.GetFileTextValue(nodeName,
Constants.FirstSequenceMumOrderNode).Split(',');
length = utilityObj.xmlUtil.GetFileTextValue(nodeName,
Constants.LengthNode).Split(',');
secondSeqOrder = utilityObj.xmlUtil.GetFileTextValue(nodeName,
Constants.SecondSequenceMumOrderNode).Split(',');
}
else
{
firstSeqOrder = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FirstSequenceMumOrderNode).Split(',');
length = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LengthNode).Split(',');
secondSeqOrder = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SecondSequenceMumOrderNode).Split(',');
}
int i = 0;
IList <MatchExtension> meNewObj = new List <MatchExtension>();
foreach (Match m in matches)
{
meNewObj.Add(new MatchExtension(m));
}
// 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)))
{
Console.WriteLine(string.Format((IFormatProvider)null,
"NUCmer BVT : Unique match not matching at index '{0}'", i.ToString((IFormatProvider)null)));
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);
}
/// <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>
static bool ValidateUniqueMatches(IList <MaxUniqueMatch> matches,
string nodeName, AdditionalParameters additionalParam, bool isFilePath)
{
switch (additionalParam)
{
case AdditionalParameters.PerformClusterBuilder:
// Validates the Cluster builder MUMs
string firstSeqOrderExpected =
Utility._xmlUtil.GetTextValue(nodeName, Constants.ClustFirstSequenceMumOrderNode);
string firstSeqStartExpected =
Utility._xmlUtil.GetTextValue(nodeName, Constants.ClustFirstSequenceStartNode);
string lengthExpected =
Utility._xmlUtil.GetTextValue(nodeName, Constants.ClustLengthNode);
string secondSeqOrderExpected =
Utility._xmlUtil.GetTextValue(nodeName, Constants.ClustSecondSequenceMumOrderNode);
string secondSeqStartExpected =
Utility._xmlUtil.GetTextValue(nodeName, Constants.ClustSecondSequenceStartNode);
StringBuilder firstSeqOrderActual = new StringBuilder();
StringBuilder firstSeqStartActual = new StringBuilder();
StringBuilder lengthActual = new StringBuilder();
StringBuilder secondSeqOrderActual = new StringBuilder();
StringBuilder secondSeqStartActual = new StringBuilder();
ClusterBuilder cb = new ClusterBuilder();
cb.MinimumScore = 0;
IList <Cluster> clusts = cb.BuildClusters(matches);
foreach (Cluster clust in clusts)
{
foreach (MaxUniqueMatchExtension maxMatchExtension in clust.Matches)
{
firstSeqOrderActual.Append(maxMatchExtension.FirstSequenceMumOrder);
secondSeqOrderActual.Append(maxMatchExtension.SecondSequenceMumOrder);
secondSeqStartActual.Append(maxMatchExtension.SecondSequenceStart);
firstSeqStartActual.Append(maxMatchExtension.FirstSequenceStart);
lengthActual.Append(maxMatchExtension.Length);
}
}
if ((0 != string.Compare(firstSeqOrderExpected.Replace(",", ""),
firstSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(firstSeqStartExpected.Replace(",", ""),
firstSeqStartActual.ToString(), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(lengthExpected.Replace(",", ""),
lengthActual.ToString(), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(secondSeqOrderExpected.Replace(",", ""),
secondSeqOrderActual.ToString(), true, CultureInfo.CurrentCulture)) ||
(0 != string.Compare(secondSeqStartExpected.Replace(",", ""),
secondSeqStartActual.ToString(), true, CultureInfo.CurrentCulture)))
{
Console.WriteLine("NUCmer BVT : Unique match not matching");
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[] firstSeqStart = null;
string[] length = null;
string[] secondSeqOrder = null;
string[] secondSeqStart = null;
if (isFilePath)
{
firstSeqOrder = Utility._xmlUtil.GetFileTextValue(nodeName,
Constants.FirstSequenceMumOrderNode).Split(',');
firstSeqStart = Utility._xmlUtil.GetFileTextValue(nodeName,
Constants.FirstSequenceStartNode).Split(',');
length = Utility._xmlUtil.GetFileTextValue(nodeName,
Constants.LengthNode).Split(',');
secondSeqOrder = Utility._xmlUtil.GetFileTextValue(nodeName,
Constants.SecondSequenceMumOrderNode).Split(',');
secondSeqStart = Utility._xmlUtil.GetFileTextValue(nodeName,
Constants.SecondSequenceStartNode).Split(',');
}
else
{
firstSeqOrder = Utility._xmlUtil.GetTextValue(nodeName,
Constants.FirstSequenceMumOrderNode).Split(',');
firstSeqStart = Utility._xmlUtil.GetTextValue(nodeName,
Constants.FirstSequenceStartNode).Split(',');
length = Utility._xmlUtil.GetTextValue(nodeName,
Constants.LengthNode).Split(',');
secondSeqOrder = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SecondSequenceMumOrderNode).Split(',');
secondSeqStart = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SecondSequenceStartNode).Split(',');
}
int i = 0;
// Loops through all the matches and validates the same.
foreach (MaxUniqueMatch match in matches)
{
if ((0 != string.Compare(firstSeqOrder[i],
match.FirstSequenceMumOrder.ToString((IFormatProvider)null), true,
CultureInfo.CurrentCulture)) ||
(0 != string.Compare(firstSeqStart[i],
match.FirstSequenceStart.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.SecondSequenceMumOrder.ToString((IFormatProvider)null), true,
CultureInfo.CurrentCulture)) ||
(0 != string.Compare(secondSeqStart[i],
match.SecondSequenceStart.ToString((IFormatProvider)null), true,
CultureInfo.CurrentCulture)))
{
Console.WriteLine(string.Format(null,
"NUCmer BVT : Unique match not matching at index '{0}'", i.ToString()));
ApplicationLog.WriteLine(string.Format(null,
"NUCmer BVT : Unique match not matching at index '{0}'", i.ToString()));
return(false);
}
i++;
}
break;
default:
break;
}
return(true);
}