public AlignmentInputData(string firstDnaString, string secondDnaString,
TransitionWeights transitionWeights)
{
FirstDnaString = firstDnaString;
SecondDnaString = secondDnaString;
TransitionWeights = transitionWeights;
}
/// <summary>
/// Преобразовать <paramref name="alignedSequence"/> в экземпляр <see cref="AlignmentResult"/>.
/// </summary>
public static AlignmentResult ToAlignmentResult(this PairwiseAlignedSequence alignedSequence,
TransitionWeights transitionWeights)
{
var indices = alignedSequence.FirstSequence
.Zip(alignedSequence.SecondSequence)
.Select((tuple, index) => (Bytes: tuple, Index: (uint)index))
.Where(tuple => tuple.Bytes.First != tuple.Bytes.Second)
.Select(tuple => tuple.Index)
.ToArray();
var alignedStrings = new AlignedStrings(
alignedSequence.FirstSequence.ToFullString(),
alignedSequence.SecondSequence.ToFullString(),
indices);
var score = alignedSequence.CalculateScore(transitionWeights);
var replacementCount = alignedSequence.FirstSequence
.Zip(alignedSequence.SecondSequence)
.Count(tuple => tuple.First != '-' && tuple.Second != '-' && tuple.First != tuple.Second);
var indelCount = alignedSequence.FirstSequence
.Concat(alignedSequence.SecondSequence)
.Count(byteValue => byteValue == '-');
return(new AlignmentResult(alignedStrings,
score,
(uint)replacementCount,
(uint)indelCount));
}
/// <summary>
/// Посчитать значение весовой функции пары выровненных последовательностей.
/// </summary>
public static long CalculateScore(this PairwiseAlignedSequence alignedSequence,
TransitionWeights transitionWeights)
{
long CalculateScorePerPair(byte leftByte, byte rightByte)
{
if (leftByte == rightByte)
{
return(transitionWeights.MatchBonus);
}
if (leftByte == '-' || rightByte == '-')
{
return(transitionWeights.IndelPenalty);
}
return(transitionWeights.MismatchPenalty);
}
long totalScore = 0;
var isFirstIndel = true;
foreach (var(leftByte, rightByte) in alignedSequence.FirstSequence.Zip(alignedSequence.SecondSequence))
{
var scorePerPair = CalculateScorePerPair(leftByte, rightByte);
if (leftByte != '-' && rightByte != '-')
{
isFirstIndel = true;
}
if (isFirstIndel &&
(leftByte == '-' || rightByte == '-') &&
transitionWeights.GapOpeningPenalty.HasValue)
{
isFirstIndel = false;
totalScore += transitionWeights.GapOpeningPenalty.Value;
}
totalScore += scorePerPair;
}
return(totalScore);
}
