/// <summary>
/// Constructor
/// </summary>
/// <param name="fastaDatabase"></param>
public SearchableDatabase(FastaDatabase fastaDatabase)
{
FastaDatabase = fastaDatabase;
_sequence = fastaDatabase.GetSequence();
_suffixArray = new int[_sequence.Length];
SAIS.sufsort(_sequence, _suffixArray, _sequence.Length);
var neighboringLcps = new byte[_suffixArray.Length];
neighboringLcps[0] = 0;
for (var i = 1; i < _suffixArray.Length; i++)
{
var lcp = IndexedDatabase.GetLcp(_sequence, _suffixArray[i - 1], _suffixArray[i]);
neighboringLcps[i] = lcp;
}
_leftLcps = new byte[_suffixArray.Length];
_rightLcps = new byte[_suffixArray.Length];
InitializeLcps(neighboringLcps, _leftLcps, _rightLcps, 0, _suffixArray.Length - 1);
}