/// <summary>
/// Initializes a new instance of the PairwiseSequenceAlignment class
/// Constructs PairwiseSequenceAlignment with input sequences
/// </summary>
/// <param name="firstSequence">First input sequence</param>
/// <param name="secondSequence">Second input sequence</param>
public PairwiseSequenceAlignment(ISequence firstSequence, ISequence secondSequence)
{
_seqAlignment = new SequenceAlignment();
_seqAlignment.Sequences.Add(firstSequence);
_seqAlignment.Sequences.Add(secondSequence);
_alignedSequences = new List <PairwiseAlignedSequence>();
}
/// <summary>
/// Initializes a new instance of the PairwiseSequenceAlignment class
/// Constructor for deserialization.
/// </summary>
/// <param name="info">Serialization Info.</param>
/// <param name="context">Streaming context.</param>
protected PairwiseSequenceAlignment(SerializationInfo info, StreamingContext context)
{
if (info == null)
{
throw new ArgumentNullException("info");
}
_alignedSequences = (List <PairwiseAlignedSequence>)info.GetValue("AlignedSeqs", typeof(List <PairwiseAlignedSequence>));
_seqAlignment = (SequenceAlignment)info.GetValue("base", typeof(SequenceAlignment));
Documentation = info.GetValue("Doc", typeof(object));
IsReadOnly = info.GetBoolean("IsReadOnly");
}
/// <summary>
/// Initializes a new instance of the PairwiseSequenceAlignment class.
/// Internal constructor to create new instance of PairwiseSequenceAlignment
/// from ISequenceAlignment.
/// </summary>
/// <param name="seqAlignment">ISequenceAlignment instance.</param>
internal PairwiseSequenceAlignment(ISequenceAlignment seqAlignment)
{
_seqAlignment = new SequenceAlignment(seqAlignment);
_alignedSequences = new List <PairwiseAlignedSequence>();
foreach (AlignedSequence alignedSeq in seqAlignment.AlignedSequences)
{
_alignedSequences.Add(new PairwiseAlignedSequence(alignedSeq));
}
// Clear the AlignedSequences in the _seqAlignment as this no longer needed.
if (!_seqAlignment.AlignedSequences.IsReadOnly)
{
_seqAlignment.AlignedSequences.Clear();
}
}
/// <summary>
/// Initializes a new instance of the PairwiseSequenceAlignment class
/// Constructs an empty PairwiseSequenceAlignment
/// </summary>
public PairwiseSequenceAlignment()
{
_seqAlignment = new SequenceAlignment();
IsReadOnly = false; // initializes to false by default, but make it explicit for good style
}
