/// <summary>
/// Copy the content to MUM.
/// </summary>
/// <param name="match">Maximum unique match.</param>
public void CopyTo(MatchExtension match)
{
if (match != null)
{
match.ReferenceSequenceMumOrder = this.ReferenceSequenceMumOrder;
match.ReferenceSequenceOffset = this.ReferenceSequenceOffset;
match.QuerySequenceMumOrder = this.QuerySequenceMumOrder;
match.QuerySequenceOffset = this.QuerySequenceOffset;
match.Length = this.Length;
match.Query = this.Query;
match.ID = this.ID;
match.IsGood = this.IsGood;
match.IsTentative = this.IsTentative;
match.Score = this.Score;
match.Adjacent = this.Adjacent;
match.From = this.From;
match.WrapScore = this.WrapScore;
}
}
/// <summary>
/// Copy the content to MUM.
/// </summary>
/// <param name="match">Maximum unique match.</param>
public void CopyTo(MatchExtension match)
{
if (match != null)
{
match.ReferenceSequenceMumOrder = this.ReferenceSequenceMumOrder;
match.ReferenceSequenceOffset = this.ReferenceSequenceOffset;
match.QuerySequenceMumOrder = this.QuerySequenceMumOrder;
match.QuerySequenceOffset = this.QuerySequenceOffset;
match.Length = this.Length;
match.Query = this.Query;
match.ID = this.ID;
match.IsGood = this.IsGood;
match.IsTentative = this.IsTentative;
match.Score = this.Score;
match.Adjacent = this.Adjacent;
match.From = this.From;
match.WrapScore = this.WrapScore;
}
}
public void ValidateMatchAndMatchExtensionToString()
{
var match = new Match();
match.Length = 20;
match.QuerySequenceOffset = 33;
var matchExtn = new MatchExtension(match);
matchExtn.ID = 1;
matchExtn.Length = 20;
string actualMatchExtnString = matchExtn.ToString();
string actualMatchstring = match.ToString();
string ExpectedMatchExtnString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.ExpectedMatchExtnStringNode);
string ExpectedMatchString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.ExpectedMatchStringNode);
Assert.AreEqual(ExpectedMatchExtnString, actualMatchExtnString);
Assert.AreEqual(actualMatchstring, ExpectedMatchString);
}
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));
}
/// <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;
}
/// <summary>
/// Process the clusters
/// </summary>
/// <param name="clusters">List of clusters</param>
/// <param name="matches">List of matches</param>
/// <param name="indexToSkip">Start index upto which match extension to be ignored.</param>
/// <param name="clusterSize">Size of cluster</param>
private void ProcessCluster(
List<Cluster> clusters,
List<MatchExtension> matches,
int indexToSkip,
int clusterSize)
{
List<MatchExtension> clusterMatches;
long total, endIndex, startIndex, score;
int counter1, counter2, counter3, best;
do
{
// remove cluster overlaps
for (counter1 = 0; counter1 < clusterSize; counter1++)
{
matches[indexToSkip + counter1].Score = matches[indexToSkip + counter1].Length;
matches[indexToSkip + counter1].Adjacent = 0;
matches[indexToSkip + counter1].From = -1;
for (counter2 = 0; counter2 < counter1; counter2++)
{
long cost, overlap, overlap1, overlap2;
overlap1 = matches[indexToSkip + counter2].ReferenceSequenceOffset
+ matches[indexToSkip + counter2].Length
- matches[indexToSkip + counter1].ReferenceSequenceOffset;
overlap = Math.Max(0, overlap1);
overlap2 = matches[indexToSkip + counter2].QuerySequenceOffset
+ matches[indexToSkip + counter2].Length -
matches[indexToSkip + counter1].QuerySequenceOffset;
overlap = Math.Max(overlap, overlap2);
// cost matches which are not on same diagonal
cost = overlap
+ Math.Abs((matches[indexToSkip + counter1].QuerySequenceOffset - matches[indexToSkip + counter1].ReferenceSequenceOffset)
- (matches[indexToSkip + counter2].QuerySequenceOffset - matches[indexToSkip + counter2].ReferenceSequenceOffset));
if (matches[indexToSkip + counter2].Score + matches[indexToSkip + counter1].Length - cost > matches[indexToSkip + counter1].Score)
{
matches[indexToSkip + counter1].From = counter2;
matches[indexToSkip + counter1].Score = matches[indexToSkip + counter2].Score
+ matches[indexToSkip + counter1].Length
- cost;
matches[indexToSkip + counter1].Adjacent = overlap;
}
}
}
// Find the match which has highest score
best = 0;
for (counter1 = 1; counter1 < clusterSize; counter1++)
{
if (matches[indexToSkip + counter1].Score > matches[indexToSkip + best].Score)
{
best = counter1;
}
}
total = 0;
endIndex = int.MinValue;
startIndex = int.MaxValue;
// TODO: remove below cast
for (counter1 = best; counter1 >= 0; counter1 = (int)matches[indexToSkip + counter1].From)
{
matches[indexToSkip + counter1].IsGood = true;
total += matches[indexToSkip + counter1].Length;
if (matches[indexToSkip + counter1].ReferenceSequenceOffset + matches[indexToSkip + counter1].Length > endIndex)
{
// Set the cluster end index
endIndex = matches[indexToSkip + counter1].ReferenceSequenceOffset + matches[indexToSkip + counter1].Length;
}
if (matches[indexToSkip + counter1].ReferenceSequenceOffset < startIndex)
{
// Set the cluster start index
startIndex = matches[indexToSkip + counter1].ReferenceSequenceOffset;
}
}
if (this.ScoreMethod == ClusterScoreMethod.MatchLength)
{
score = total;
}
else
{
score = endIndex - startIndex;
}
// If the current score exceeds the minimum score
// and the matches to cluster
if (score >= this.MinimumScore)
{
clusterMatches = new List<MatchExtension>();
for (counter1 = 0; counter1 < clusterSize; counter1++)
{
if (matches[indexToSkip + counter1].IsGood)
{
MatchExtension match = matches[indexToSkip + counter1];
if (matches[indexToSkip + counter1].Adjacent != 0)
{
match = new MatchExtension();
matches[indexToSkip + counter1].CopyTo(match);
match.ReferenceSequenceOffset += match.Adjacent;
match.QuerySequenceOffset += match.Adjacent;
match.Length -= match.Adjacent;
}
clusterMatches.Add(match);
}
}
// adding the cluster to list
if (0 < clusterMatches.Count)
{
clusters.Add(new Cluster(clusterMatches));
}
}
// Correcting the cluster indices
for (counter1 = counter3 = 0; counter1 < clusterSize; counter1++)
{
if (!matches[indexToSkip + counter1].IsGood)
{
if (counter1 != counter3)
{
matches[indexToSkip + counter3] = matches[indexToSkip + counter1];
}
counter3++;
}
}
clusterSize = counter3;
}
while (clusterSize > 0);
}
public void TestMatchAndMatchExtensionToString()
{
Match match = new Match();
match.Length = 20;
match.QuerySequenceOffset = 33;
MatchExtension matchExtn = new MatchExtension(match);
matchExtn.ID = 1;
matchExtn.Length = 20;
string actualMatchExtnString = matchExtn.ToString();
string actualMatchstring = match.ToString();
string ExpectedMatchExtnString = "RefStart=0 QueryStart=33 Length=20 Score=0 WrapScore=0 IsGood=False";
string ExpectedMatchString = "RefStart=0 QueryStart=33 Length=20";
Assert.AreEqual(ExpectedMatchExtnString, actualMatchExtnString);
Assert.AreEqual(actualMatchstring, ExpectedMatchString);
}
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);
}
