/// <summary>
/// this is the function you implement.
/// </summary>
/// <param name="sequenceA">the first sequence</param>
/// <param name="sequenceB">the second sequence, may have length not equal to the length of the first seq.</param>
/// <param name="banded">true if alignment should be band limited.</param>
/// <returns>the alignment score and the alignment (in a Result object) for sequenceA and sequenceB. The calling function places the result in the dispay appropriately.
///
public ResultTable.Result Align_And_Extract(Tuple<int,int> cell, GeneSequence sequenceA, GeneSequence sequenceB, bool banded)
{
ResultTable.Result result = new ResultTable.Result();
int score; // place your computed alignment score here
string[] alignment = new string[2]; // place your two computed alignments here
// ********* these are placeholder assignments that you'll replace with your code *******
string a = sequenceA.Sequence.Substring(0, sequenceA.Sequence.Length < MaxCharactersToAlign ? sequenceA.Sequence.Length : MaxCharactersToAlign);
string b = sequenceB.Sequence.Substring(0, sequenceB.Sequence.Length < MaxCharactersToAlign ? sequenceB.Sequence.Length : MaxCharactersToAlign);
DynamicProgramming dp = new DynamicProgramming(cell, a, b, banded);
score = dp.getScore();
alignment[0] = dp.getResultA();
alignment[1] = dp.getResultB();
// ***************************************************************************************
result.Update(score,alignment[0],alignment[1]); // bundling your results into the right object type
return(result);
}
/// <summary>
/// this is the function you implement.
/// </summary>
/// <param name="sequenceA">the first sequence</param>
/// <param name="sequenceB">the second sequence, may have length not equal to the length of the first seq.</param>
/// <param name="banded">true if alignment should be band limited.</param>
/// <returns>the alignment score and the alignment (in a Result object) for sequenceA and sequenceB. The calling function places the result in the dispay appropriately.
///
public ResultTable.Result Align_And_Extract(Tuple <int, int> cell, GeneSequence sequenceA, GeneSequence sequenceB, bool banded)
{
ResultTable.Result result = new ResultTable.Result();
int score; // place your computed alignment score here
string[] alignment = new string[2]; // place your two computed alignments here
// ********* these are placeholder assignments that you'll replace with your code *******
string a = sequenceA.Sequence.Substring(0, sequenceA.Sequence.Length < MaxCharactersToAlign ? sequenceA.Sequence.Length : MaxCharactersToAlign);
string b = sequenceB.Sequence.Substring(0, sequenceB.Sequence.Length < MaxCharactersToAlign ? sequenceB.Sequence.Length : MaxCharactersToAlign);
DynamicProgramming dp = new DynamicProgramming(cell, a, b, banded);
score = dp.getScore();
alignment[0] = dp.getResultA();
alignment[1] = dp.getResultB();
// ***************************************************************************************
result.Update(score, alignment[0], alignment[1]); // bundling your results into the right object type
return(result);
}