/// <summary>
/// Builds difference list from match list
/// </summary>
/// <param name="matchList">List of matching segments</param>
/// <param name="sequence1">First sequence</param>
/// <param name="sequence2">Second sequence</param>
/// <returns>List of difference nodes</returns>
public static List <DifferenceNode> BuildDiffList(List <WordMatch> matchList, ISequence sequence1, ISequence sequence2)
{
// Sort match list according to start indices
matchList.Sort(CompareDifferenceNode);
List <DifferenceNode> diffList = new List <DifferenceNode>();
int mismatchStart1, mismatchStart2, mismatchEnd1, mismatchEnd2;
mismatchStart1 = 0;
mismatchStart2 = 0;
// There might be some mutation at starting
WordMatch first = matchList[0];
if (first.Sequence1Start > 0 || first.Sequence2Start > 0)
{
diffList.Add(new DifferenceNode(0, 0, first.Sequence1Start - 1, first.Sequence2Start - 1));
}
// Primer for starting iteration
matchList.RemoveAt(0);
mismatchStart1 = first.Sequence1Start + first.Length;
mismatchStart2 = first.Sequence2Start + first.Length;
foreach (WordMatch n in matchList)
{
mismatchEnd1 = n.Sequence1Start - 1;
mismatchEnd2 = n.Sequence2Start - 1;
diffList.Add(new DifferenceNode(mismatchStart1, mismatchStart2, mismatchEnd1, mismatchEnd2));
mismatchStart1 = n.Sequence1Start + n.Length;
mismatchStart2 = n.Sequence2Start + n.Length;
}
// There might be some mutation at the end
mismatchEnd1 = sequence1.Count - 1;
mismatchEnd2 = sequence2.Count - 1;
if (mismatchStart1 <= mismatchEnd1 || mismatchStart2 <= mismatchEnd2)
{
diffList.Add(new DifferenceNode(mismatchStart1, mismatchStart2, mismatchEnd1, mismatchEnd2));
}
return(diffList);
}
/// <summary>
/// Comparison of two word match list nodes
/// based on the first sequence start indices
/// </summary>
/// <param name="n1">First match list node</param>
/// <param name="n2">Second match list node</param>
/// <returns>Integer value indicating zero if equal.</returns>
public static int CompareDifferenceNode(WordMatch n1, WordMatch n2)
{
return(n1.Sequence1Start - n2.Sequence1Start);
}