/// <summary>
/// Main Edlib method.
/// </summary>
/// <param name="originalQuery">String a</param>
/// <param name="originalTarget">String b</param>
/// <param name="config">Configuration</param>
/// <returns>Result of the alignment</returns>
public static AlignmentResult Align(string originalQuery, string originalTarget, AlignmentConfig config)
{
// NOTE: Is other mode useful? If so, why?
if (config.Mode == AlignmentMode.Hw || config.Mode == AlignmentMode.Shw)
{
throw new NotImplementedException();
}
AlignmentResult result = new AlignmentResult
{
Status = (int)AlignmentStatus.Ok,
EditDistance = -1,
EndLocations = null,
StartingLocations = null,
NumberOfLocations = 0,
Alignment = null,
AlignmentLength = 0,
AlphabetLength = 0,
};
// Transform sequences and recognize alphabet
byte[] query, target;
string alphabet = TransformSequences(originalQuery, originalTarget, out query, out target);
result.AlphabetLength = alphabet.Length;
// Initialization
int queryLength = originalQuery.Length;
int targetLength = originalTarget.Length;
int maxBlocks = CeilDivision(queryLength, WordSize);
int w = maxBlocks * WordSize - queryLength;
EqualityDefinition equalityDefinition = new EqualityDefinition(alphabet, config.AdditionalEqualities,
config.AdditionalEqualitiesLength);
ulong[] peq = BuildPeq(alphabet.Length, query, queryLength, ref equalityDefinition);
// Main Calculation
int positionNw = -1;
AlignmentData alignmentData = new AlignmentData();
bool dynamicK = false;
int k = config.K;
if (k < 0) // If valid k is not given, auto-adjust k until solution is found.
{
dynamicK = true;
k = WordSize; // Gives better results than smaller k.
}
do
{
MyersEditDistanceNw(peq, w, maxBlocks, queryLength, target, targetLength, k, false, -1,
ref result.EditDistance, ref positionNw, ref alignmentData);
k *= 2;
} while (dynamicK && result.EditDistance == -1);
// NOTE: Do we need this block code? We only care about editing distance
// Since we only care about the editing distance score, this is where we stop
if (result.EditDistance >= 0)
{
// If NW mode, set end location explicitly.
if (config.Mode == AlignmentMode.Nw)
{
result.EndLocations = new int[sizeof(int) * 1];
result.EndLocations[0] = targetLength - 1;
result.NumberOfLocations = 1;
}
// if (!(config.Task == AlignmentTask.TaskLocate || config.Task == AlignmentTask.TaskPath))
// {
// for (int i = 0; i < result.NumberOfLocations; i++) {
// result.StartingLocations[i] = 0;
// }
// }
}
return(result);
}
/// <summary>
/// Build Peq table for given query and alphabet.
/// Peq is table of dimensions alphabetLength+1 x maxNumBlocks.
/// Bit i of Peq[s * maxNumBlocks + b] is 1 if i-th symbol from block b of query equals symbol s, otherwise it is 0.
/// </summary>
/// <param name="alphabetLength"></param>
/// <param name="query"></param>
/// <param name="queryLength"></param>
/// <param name="equalityDefinition"></param>
/// <returns>Table of dimensions alphabetLength+1 x maxNumBlocks.</returns>
private static ulong[] BuildPeq(int alphabetLength, byte[] query, int queryLength, ref EqualityDefinition equalityDefinition)
{
int maxBlocks = CeilDivision(queryLength, WordSize);
// Table of dimensions alphabetLength+1 x maxNumBlocks. Last symbol is wildcard.
ulong[] peq = new ulong[(alphabetLength + 1) * maxBlocks];
// Build Peq (1 is match, 0 is mismatch). NOTE: last column is wildcard(symbol that matches anything) with just 1s
for (byte symbol = 0; symbol <= alphabetLength; symbol++)
{
for (int b = 0; b < maxBlocks; b++)
{
if (symbol < alphabetLength)
{
peq[symbol * maxBlocks + b] = 0;
for (int r = (b + 1) * WordSize - 1; r >= b * WordSize; r--)
{
peq[symbol * maxBlocks + b] <<= 1;
// NOTE: We pretend like query is padded at the end with W wildcard symbols
if (r >= queryLength || equalityDefinition.IsEqual(query[r], symbol))
{
peq[symbol * maxBlocks + b] += 1;
}
}
}
else
{
peq[symbol * maxBlocks + b] = UInt64.MaxValue;
}
}
}
return(peq);
}
