protected static Alignment <string, char> CreateAlignment(params string[] alignment)
{
var sequences = new Tuple <string, AlignmentCell <char>, IEnumerable <AlignmentCell <char> >, AlignmentCell <char> > [alignment.GetLength(0)];
for (int i = 0; i < alignment.Length; i++)
{
var sb = new StringBuilder();
string[] split = alignment[i].Split('|');
string prefix = split[0].Trim();
sb.Append(prefix);
string[] cellStrs = split[1].Trim().Split(new[] { ' ' }, StringSplitOptions.RemoveEmptyEntries);
var cells = new AlignmentCell <char> [cellStrs.Length];
for (int j = 0; j < cellStrs.Length; j++)
{
if (cellStrs[j] == "-")
{
cells[j] = new AlignmentCell <char>();
}
else
{
sb.Append(cellStrs[j]);
cells[j] = new AlignmentCell <char>(cellStrs[j]);
}
}
string suffix = split[2].Trim();
sb.Append(suffix);
sequences[i] = Tuple.Create(sb.ToString(), new AlignmentCell <char>(prefix), (IEnumerable <AlignmentCell <char> >)cells, new AlignmentCell <char>(suffix));
}
return(new Alignment <string, char>(0, 0, sequences));
}
public Alignment(int rawScore, double normalizedScore, IEnumerable <Tuple <TSeq, AlignmentCell <TItem>, IEnumerable <AlignmentCell <TItem> >, AlignmentCell <TItem> > > sequences)
{
if (double.IsNaN(normalizedScore) || normalizedScore < 0 || normalizedScore > 1)
{
throw new ArgumentOutOfRangeException("normalizedScore");
}
Tuple <TSeq, AlignmentCell <TItem>, IEnumerable <AlignmentCell <TItem> >, AlignmentCell <TItem> >[] sequenceArray = sequences.ToArray();
if (sequenceArray.Length == 0)
{
throw new ArgumentException("No sequences specified.", "sequences");
}
_rawScore = rawScore;
_normalizedScore = normalizedScore;
var seqs = new TSeq[sequenceArray.Length];
var prefixes = new AlignmentCell <TItem> [sequenceArray.Length];
var suffixes = new AlignmentCell <TItem> [sequenceArray.Length];
for (int i = 0; i < sequenceArray.Length; i++)
{
seqs[i] = sequenceArray[i].Item1;
prefixes[i] = sequenceArray[i].Item2;
AlignmentCell <TItem>[] columnArray = sequenceArray[i].Item3.ToArray();
if (_matrix == null)
{
_matrix = new AlignmentCell <TItem> [sequenceArray.Length, columnArray.Length];
}
else if (columnArray.Length != _matrix.GetLength(1))
{
throw new ArgumentException("All sequences are not the same length.", "sequences");
}
for (int j = 0; j < columnArray.Length; j++)
{
_matrix[i, j] = columnArray[j];
}
suffixes[i] = sequenceArray[i].Item4;
}
_sequences = new ReadOnlyList <TSeq>(seqs);
_prefixes = new ReadOnlyList <AlignmentCell <TItem> >(prefixes);
_suffixes = new ReadOnlyList <AlignmentCell <TItem> >(suffixes);
}