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 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_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 AlignEmptySequence()
{
var scorer = new StringScorer();
var msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "car", "", "bar" }, GetChars)
{
UseInputOrder = true
};
msa.Compute();
Alignment <string, char> alignment = msa.GetAlignment();
AssertAlignmentsEqual(alignment, CreateAlignment(
"| c a r |",
"| - - - |",
"| b a r |"
));
}
public void AlignLessThanThreeSequences()
{
var scorer = new StringScorer();
Assert.Throws <ArgumentException>(() =>
{
var msa = new MultipleAlignmentAlgorithm <string, char>(scorer, Enumerable.Empty <string>(), GetChars);
});
Assert.Throws <ArgumentException>(() =>
{
var msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "bar" }, GetChars);
});
Assert.Throws <ArgumentException>(() =>
{
var msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "car", "bar" }, GetChars);
});
}
public void AlignMoreThanTwoSequences()
{
var scorer = new StringScorer();
var msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "car", "bar", "carp" }, GetChars)
{
UseInputOrder = true
};
msa.Compute();
Alignment <string, char> alignment = msa.GetAlignment();
AssertAlignmentsEqual(alignment, CreateAlignment(
"| c a r - |",
"| b a r - |",
"| c a r p |"
));
msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "car", "bar", "star" }, GetChars)
{
UseInputOrder = true
};
msa.Compute();
alignment = msa.GetAlignment();
AssertAlignmentsEqual(alignment, CreateAlignment(
"| - c a r |",
"| - b a r |",
"| s t a r |"
));
msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "car", "bar", "stare" }, GetChars)
{
UseInputOrder = true
};
msa.Compute();
alignment = msa.GetAlignment();
AssertAlignmentsEqual(alignment, CreateAlignment(
"| - c a r - |",
"| - b a r - |",
"| s t a r e |"
));
msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "scar", "car", "bar", "stare" }, GetChars)
{
UseInputOrder = true
};
msa.Compute();
alignment = msa.GetAlignment();
AssertAlignmentsEqual(alignment, CreateAlignment(
"| s c a r - |",
"| - c a r - |",
"| - b a r - |",
"| s t a r e |"
));
msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "sane", "scar", "car", "bar", "stare" }, GetChars)
{
UseInputOrder = true
};
msa.Compute();
alignment = msa.GetAlignment();
AssertAlignmentsEqual(alignment, CreateAlignment(
"| s - a n e |",
"| s c a r - |",
"| - c a r - |",
"| - b a r - |",
"| s t a r e |"
));
msa = new MultipleAlignmentAlgorithm <string, char>(scorer, new[] { "sane", "scar", "she", "car", "bar", "stare" }, GetChars)
{
UseInputOrder = true
};
msa.Compute();
alignment = msa.GetAlignment();
AssertAlignmentsEqual(alignment, CreateAlignment(
"| s - a n e |",
"| s c a r - |",
"| s - - h e |",
"| - c a r - |",
"| - b a r - |",
"| s t a r e |"
));
}
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));
}
