public void SemiGlobalAlign()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "car", "bar", GetChars)
{
Mode = AlignmentMode.SemiGlobal
};
msa.Compute();
Alignment <string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.66).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "cart", "bar", GetChars)
{
Mode = AlignmentMode.SemiGlobal
};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r | t",
"| b a r | "
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.57).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "cart", "art", GetChars)
{
Mode = AlignmentMode.SemiGlobal
};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"c | a r t |",
" | a r t |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.86).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "start", "tan", GetChars)
{
Mode = AlignmentMode.SemiGlobal
};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"s | t a r | t",
" | t a n | "
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.50).Within(0.01));
}
public WordAlignmentMatrix GetBestAlignment(IReadOnlyList <string> sourceSegment, IReadOnlyList <string> targetSegment,
WordAlignmentMatrix hintMatrix = null)
{
var paa = new PairwiseAlignmentAlgorithm <IReadOnlyList <string>, int>(_scorer, sourceSegment, targetSegment, GetWordIndices)
{
Mode = AlignmentMode.Global,
ExpansionCompressionEnabled = true,
TranspositionEnabled = true
};
paa.Compute();
Alignment <IReadOnlyList <string>, int> alignment = paa.GetAlignments().First();
var waMatrix = new WordAlignmentMatrix(sourceSegment.Count, targetSegment.Count);
for (int c = 0; c < alignment.ColumnCount; c++)
{
foreach (int i in alignment[0, c])
{
foreach (int j in alignment[1, c])
{
waMatrix[i, j] = AlignmentType.Aligned;
}
}
}
return(waMatrix);
}
public void GlobalAlign()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "car", "bar", GetChars);
msa.Compute();
Alignment <string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.66).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "cart", "bar", GetChars);
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r t |",
"| b a r - |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.25).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "cart", "art", GetChars);
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r t |",
"| - a r t |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.50).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "start", "tan", GetChars);
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(2));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| s t a r t |",
"| - t a - n |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.00).Within(0.01));
AssertAlignmentsEqual(alignments[1], CreateAlignment(
"| s t a r t |",
"| - t a n - |"
));
Assert.That(alignments[1].NormalizedScore, Is.EqualTo(0.00).Within(0.01));
}
public void GlobalAlign()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "car", "bar", GetChars);
msa.Compute();
Alignment<string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.66).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "cart", "bar", GetChars);
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r t |",
"| b a r - |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.25).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "cart", "art", GetChars);
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r t |",
"| - a r t |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.50).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "start", "tan", GetChars);
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(2));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| s t a r t |",
"| - t a - n |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.00).Within(0.01));
AssertAlignmentsEqual(alignments[1], CreateAlignment(
"| s t a r t |",
"| - t a n - |"
));
Assert.That(alignments[1].NormalizedScore, Is.EqualTo(0.00).Within(0.01));
}
public void ExpansionCompressionAlign()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "car", "bar", GetChars) {ExpansionCompressionEnabled = true};
msa.Compute();
Alignment<string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.66).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "cart", "bar", GetChars) {ExpansionCompressionEnabled = true};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a rt |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.50).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "cart", "art", GetChars) {ExpansionCompressionEnabled = true};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| ca r t |",
"| a r t |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.75).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "start", "tan", GetChars) {ExpansionCompressionEnabled = true};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(2));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| st ar t |",
"| t a n |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.40).Within(0.01));
AssertAlignmentsEqual(alignments[1], CreateAlignment(
"| st a rt |",
"| t a n |"
));
Assert.That(alignments[1].NormalizedScore, Is.EqualTo(0.40).Within(0.01));
}
public void GlobalAlign_EmptySequence()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "", "", GetChars);
msa.Compute();
Alignment <string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"||",
"||"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0));
}
public void ZeroMaxScore()
{
var scorer = new ZeroMaxScoreStringScorer();
var msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "car", "bar", GetChars)
{
ExpansionCompressionEnabled = true
};
msa.Compute();
Alignment <string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0));
}
public override IEnumerable <Alignment <Word, ShapeNode> > GetAlignments()
{
return(_algorithm.GetAlignments());
}
public WordAlignmentMatrix GetBestAlignment(IReadOnlyList <string> sourceSegment,
IReadOnlyList <string> targetSegment, WordAlignmentMatrix hintMatrix = null)
{
var paa = new PairwiseAlignmentAlgorithm <IReadOnlyList <string>, int>(_scorer, sourceSegment, targetSegment,
GetWordIndices)
{
Mode = AlignmentMode.Global,
ExpansionCompressionEnabled = true,
TranspositionEnabled = true
};
paa.Compute();
Alignment <IReadOnlyList <string>, int> alignment = paa.GetAlignments().First();
var waMatrix = new WordAlignmentMatrix(sourceSegment.Count, targetSegment.Count);
for (int c = 0; c < alignment.ColumnCount; c++)
{
foreach (int j in alignment[1, c])
{
double bestScore;
int minIndex, maxIndex;
if (alignment[0, c].IsNull)
{
double prob = _getTranslationProb(null, targetSegment[j]);
bestScore = ComputeAlignmentScore(prob, 0);
int tc = c - 1;
while (tc >= 0 && alignment[0, tc].IsNull)
{
tc--;
}
int i = tc == -1 ? 0 : alignment[0, tc].Last;
minIndex = i;
maxIndex = i + 1;
}
else
{
double prob = alignment[0, c]
.Average(i => _getTranslationProb(sourceSegment[i], targetSegment[j]));
bestScore = ComputeAlignmentScore(prob, 0);
minIndex = alignment[0, c].First - 1;
maxIndex = alignment[0, c].Last + 1;
}
int bestIndex = -1;
for (int i = minIndex; i >= Math.Max(0, minIndex - _maxDistance); i--)
{
double prob = _getTranslationProb(sourceSegment[i], targetSegment[j]);
double distanceScore = ComputeDistanceScore(i, minIndex + 1, sourceSegment.Count);
double score = ComputeAlignmentScore(prob, distanceScore);
if (score > bestScore)
{
bestScore = score;
bestIndex = i;
}
}
for (int i = maxIndex; i < Math.Min(sourceSegment.Count, maxIndex + _maxDistance); i++)
{
double prob = _getTranslationProb(sourceSegment[i], targetSegment[j]);
double distanceScore = ComputeDistanceScore(i, maxIndex - 1, sourceSegment.Count);
double score = ComputeAlignmentScore(prob, distanceScore);
if (score > bestScore)
{
bestScore = score;
bestIndex = i;
}
}
if (bestIndex == -1)
{
if (!alignment[0, c].IsNull)
{
waMatrix[minIndex + 1, j] = AlignmentType.Aligned;
waMatrix[maxIndex - 1, j] = AlignmentType.Aligned;
}
}
else
{
waMatrix[bestIndex, j] = AlignmentType.Aligned;
}
}
}
return(waMatrix);
}
public void ExpansionCompressionAlign()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "car", "bar", GetChars)
{
ExpansionCompressionEnabled = true
};
msa.Compute();
Alignment <string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.66).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "cart", "bar", GetChars)
{
ExpansionCompressionEnabled = true
};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a rt |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.50).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "cart", "art", GetChars)
{
ExpansionCompressionEnabled = true
};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| ca r t |",
"| a r t |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.75).Within(0.01));
msa = new PairwiseAlignmentAlgorithm <string, char>(scorer, "start", "tan", GetChars)
{
ExpansionCompressionEnabled = true
};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(2));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| st ar t |",
"| t a n |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.40).Within(0.01));
AssertAlignmentsEqual(alignments[1], CreateAlignment(
"| st a rt |",
"| t a n |"
));
Assert.That(alignments[1].NormalizedScore, Is.EqualTo(0.40).Within(0.01));
}
public void ZeroMaxScore()
{
var scorer = new ZeroMaxScoreStringScorer();
var msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "car", "bar", GetChars) {ExpansionCompressionEnabled = true};
msa.Compute();
Alignment<string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0));
}
public void SemiGlobalAlign_EmptySequence()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "", "", GetChars) {Mode = AlignmentMode.SemiGlobal};
msa.Compute();
Alignment<string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"||",
"||"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0));
}
public void SemiGlobalAlign()
{
var scorer = new StringScorer();
var msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "car", "bar", GetChars) {Mode = AlignmentMode.SemiGlobal};
msa.Compute();
Alignment<string, char>[] alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r |",
"| b a r |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.66).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "cart", "bar", GetChars) {Mode = AlignmentMode.SemiGlobal};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"| c a r | t",
"| b a r | "
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.57).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "cart", "art", GetChars) {Mode = AlignmentMode.SemiGlobal};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"c | a r t |",
" | a r t |"
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.86).Within(0.01));
msa = new PairwiseAlignmentAlgorithm<string, char>(scorer, "start", "tan", GetChars) {Mode = AlignmentMode.SemiGlobal};
msa.Compute();
alignments = msa.GetAlignments().ToArray();
Assert.That(alignments.Length, Is.EqualTo(1));
AssertAlignmentsEqual(alignments[0], CreateAlignment(
"s | t a r | t",
" | t a n | "
));
Assert.That(alignments[0].NormalizedScore, Is.EqualTo(0.50).Within(0.01));
}