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 MultipleAlignmentAlgorithm(IPairwiseAlignmentScorer <TSeq, TItem> scorer, IEnumerable <TSeq> sequences, ItemsSelector <TSeq, TItem> itemsSelector)
{
_scorer = scorer;
_sequences = sequences.ToArray();
if (_sequences.Length < 3)
{
throw new ArgumentException("At least three sequences must be specified.", "sequences");
}
_itemsSelector = itemsSelector;
}
public PairwiseAlignmentAlgorithm(IPairwiseAlignmentScorer <TSeq, TItem> scorer, TSeq sequence1, TSeq sequence2, ItemsSelector <TSeq, TItem> itemsSelector)
{
_scorer = scorer;
_sequence1 = sequence1;
_items1 = itemsSelector(sequence1, out _startIndex1, out _count1).ToArray();
_sequence2 = sequence2;
_items2 = itemsSelector(sequence2, out _startIndex2, out _count2).ToArray();
_sim = new int[_count1 + 1, _count2 + 1];
_gapPenalty = scorer.GetGapPenalty(sequence1, sequence2);
}
public PairwiseWordAlignerResult(IWordAligner wordAligner, IPairwiseAlignmentScorer <Word, ShapeNode> scorer, WordPairAlignerSettings settings, Word word1, Word word2)
: base(wordAligner)
{
_words = new ReadOnlyList <Word>(new [] { word1, word2 });
_algorithm = new PairwiseAlignmentAlgorithm <Word, ShapeNode>(scorer, word1, word2, GetNodes)
{
ExpansionCompressionEnabled = settings.ExpansionCompressionEnabled,
Mode = settings.Mode
};
_algorithm.Compute();
}
public PairwiseWordAlignerResult(IWordAligner wordAligner, IPairwiseAlignmentScorer<Word, ShapeNode> scorer, WordPairAlignerSettings settings, Word word1, Word word2)
: base(wordAligner)
{
_words = new ReadOnlyList<Word>(new [] {word1, word2});
_algorithm = new PairwiseAlignmentAlgorithm<Word, ShapeNode>(scorer, word1, word2, GetNodes)
{
ExpansionCompressionEnabled = settings.ExpansionCompressionEnabled,
Mode = settings.Mode
};
_algorithm.Compute();
}
public ProfileScorer(IPairwiseAlignmentScorer <TSeq, TItem> scorer)
{
_scorer = scorer;
}
