public MultipleWordAlignerResult(IWordAligner wordAligner, IPairwiseAlignmentScorer<Word, ShapeNode> scorer, IEnumerable<Word> words)
: base(wordAligner)
{
_words = new ReadOnlyList<Word>(words.ToArray());
_algorithm = new MultipleAlignmentAlgorithm<Word, ShapeNode>(scorer, _words, GetNodes);
_algorithm.Compute();
}
public MultipleWordAlignerResult(IWordAligner wordAligner, IPairwiseAlignmentScorer <Word, ShapeNode> scorer, IEnumerable <Word> words)
: base(wordAligner)
{
_words = new ReadOnlyList <Word>(words.ToArray());
_algorithm = new MultipleAlignmentAlgorithm <Word, ShapeNode>(scorer, _words, GetNodes);
_algorithm.Compute();
}
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 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 ZeroMaxScore()
{
var scorer = new ZeroMaxScoreStringScorer();
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 |"
));
Assert.That(alignment.NormalizedScore, Is.EqualTo(0));
}
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 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 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 ZeroMaxScore()
{
var scorer = new ZeroMaxScoreStringScorer();
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 |"
));
Assert.That(alignment.NormalizedScore, Is.EqualTo(0));
}
