/// <summary>
/// Computes the longest common subsequence of the two sequences.
/// </summary>
/// <param name="source">The source sequence</param>
/// <param name="target">The target sequence</param>
/// <param name="minLength">The minimum length of an aligned substring</param>
/// <param name="scorer">The score provider to use</param>
/// <param name="picker">An extension disambiguator (may be null)</param>
public static List <AlignedSubstring> ComputeLongestCommonSubsequence(IList <T> source,
IList <T> target, int minLength,
ISequenceAlignmentItemScoreProvider <T> scorer,
IExtensionDisambiguator picker)
{
return(ComputeCoverage(source, target, minLength, scorer, picker, 1));
}
/// <summary>
/// Computes the longest local alignment coverage of the two sequences.
/// </summary>
/// <param name="source">The source sequence</param>
/// <param name="target">The target sequence</param>
/// <param name="scorer">The score provider to use</param>
/// <param name="picker">An extension disambiguator (may be null)</param>
public static List <AlignedSubstring> ComputeCoverage(IList <T> source,
IList <T> target,
ISequenceAlignmentItemScoreProvider <T> scorer,
IExtensionDisambiguator picker)
{
return(ComputeCoverage(source, target, 1, scorer, picker, 0));
}
/// <summary>
/// Computes the longest local alignment coverage of the two sequences.
/// </summary>
/// <param name="source">The source sequence</param>
/// <param name="target">The target sequence</param>
/// <param name="minLength">The minimum length of an aligned substring</param>
/// <param name="scorer">The score provider to use</param>
/// <param name="picker">An extension disambiguator (may be null)</param>
/// <param name="maxItems">The maximum number of items in the result coverage. If 1,
/// no coverage, but only the longest subsequence will be computed. If 0, the full
/// coverage will be computed.</param>
public static List <AlignedSubstring> ComputeCoverage(IList <T> source,
IList <T> target, int minLength,
ISequenceAlignmentItemScoreProvider <T> scorer,
IExtensionDisambiguator picker,
int maxItems)
{
SequenceAlignmentComputer <T> aligner = new SequenceAlignmentComputer <T>(source,
target, scorer, picker, minLength, maxItems);
return(aligner.Compute());
}
/// <summary>
/// Initializes a new instance with the provided values. Once initialized,
/// call <see cref="Compute()"/> to compute and return the actual alignment.
/// </summary>
/// <param name="source">The source sequence</param>
/// <param name="target">The target sequence</param>
/// <param name="scorer">The score provider to use</param>
/// <param name="picker">An extension disambiguator (may be null)</param>
/// <param name="minLength">The minimum length of an aligned substring</param>
/// <param name="maxItems">The maximum number of items in the result coverage. If 1,
/// no coverage, but only the longest subsequence will be computed. If 0, the full
/// coverage will be computed.</param>
public SequenceAlignmentComputer(IList <T> source,
IList <T> target,
ISequenceAlignmentItemScoreProvider <T> scorer,
IExtensionDisambiguator picker,
int minLength,
int maxItems)
{
if (source == null)
{
throw new ArgumentNullException("source");
}
if (target == null)
{
throw new ArgumentNullException("target");
}
if (scorer == null)
{
throw new ArgumentNullException("scorer");
}
if (minLength <= 0)
{
minLength = 1;
}
if (maxItems < 0)
{
maxItems = 0;
}
_MinLength = minLength;
_MaxItems = maxItems;
_Source = source;
_Target = target;
_Scorer = scorer;
_Picker = picker;
}
