/// <summary>
/// Computes the longest common substrings of two input sequences of a common element type <typeparamref name="T"/>. To compare
/// the items, .Equal() is called on the objects. A longest common substring is always
/// contiguous (unlike the longest common subsequence, which is not necessarily continguous). This method
/// will compute the broadest coverage for the input sequences. This means that first the longest substring
/// is found. Unlike <see cref="ComputeLongestCommonSubstring"/>, the search is then continued and more (possibly shorter)
/// longest substrings are identified in the remainder (uncovered portion) of the string. Note that the
/// coverage is not necessarily optimal - if more than one longest common substring exists during any
/// iteration, the first one found is picked which may lead to a suboptimal overall coverage.
/// </summary>
/// <param name="sequenceA">The first (source) sequence</param>
/// <param name="sequenceB">The second (target) sequence</param>
/// <returns>A list of substring objects, which can be null (null/empty argument), empty (no common
/// substring), or contain a good coverage of the input sequences.
/// </returns>
public static List <AlignedSubstring> ComputeLongestCommonSubstringCoverage(IList <T> sequenceA,
IList <T> sequenceB)
{
// http://en.wikipedia.org/wiki/Longest_common_substring_problem
if (sequenceA == null || sequenceA.Count == 0 ||
sequenceB == null || sequenceB.Count == 0)
{
return(null);
}
List <AlignedSubstring> result = SequenceAlignmentComputer <T> .ComputeCoverage(sequenceA,
sequenceB, new SimpleLCSScoreProvider <T>(), null);
#if DEBUG
if (result != null && result.Count > 0)
{
foreach (AlignedSubstring s in result)
{
System.Diagnostics.Debug.Assert(s.Source.Length == s.Target.Length);
System.Diagnostics.Debug.Assert(s.Source.Start >= 0 && s.Source.Start < sequenceA.Count);
System.Diagnostics.Debug.Assert(s.Target.Start >= 0 && s.Target.Start < sequenceB.Count);
for (int p = 0; p < s.Source.Length; ++p)
{
System.Diagnostics.Debug.Assert(sequenceA[s.Source.Start + p].Equals(sequenceB[s.Target.Start + p]));
}
}
}
#endif
return(result);
}
/// <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());
}
