/// <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="resultTableSoFar">the table of alignment results that has been generated so far using pair-wise alignment</param>
/// <param name="rowInTable">this particular alignment problem will occupy a cell in this row the result table.</param>
/// <param name="columnInTable">this particular alignment will occupy a cell in this column of the result table.</param>
/// <returns>the alignment score for sequenceA and sequenceB. The calling function places the result in entry rowInTable,columnInTable
/// of the ResultTable</returns>
public int Align(GeneSequence sequenceA, GeneSequence sequenceB, ResultTable resultTableSoFar, int rowInTable, int columnInTable)
{
if((columnInTable - rowInTable) < 0)
{
return 0;
}
Grid grid = new Grid(sequenceA.Sequence, sequenceB.Sequence, true, MaxCharactersToAlign);
return grid.CalculateScoreSolution();
}
private void dataGridViewResults_CellMouseClick(object sender, DataGridViewCellMouseEventArgs e)
{
statusMessage.Text = "Calculating Alignment...";
txtAlignment.Text = "";
this.Refresh();
Grid extractionGrid = new Grid(m_sequences[e.RowIndex].Sequence, m_sequences[e.ColumnIndex].Sequence, false, 5000);
int score = extractionGrid.CalculateExtractionSolution();
Tuple<string, string> sequences = extractionGrid.ExtractPath();
string trimmedNewTopSequence = TrimAlignment(sequences.Item1);
string trimmedNewLeftSequence = TrimAlignment(sequences.Item2);
StringBuilder builder = new StringBuilder();
builder.Append(FormatSequence(trimmedNewTopSequence));
builder.Append(FormatSequence(trimmedNewLeftSequence));
txtAlignment.Text = builder.ToString();
statusMessage.Text = "Done.";
}