private void button1_Click(object sender, EventArgs e)
{
// remove whitespace and prepend a - to contents of seq
char[] first = ("-" + Regex.Replace(seq1.Text, @"\s+", "").ToUpper()).ToCharArray();
char[] second = ("-" + Regex.Replace(seq2.Text, @"\s+", "").ToUpper()).ToCharArray();
int[] scoreSystem = new int[3];
if (countGaps.Checked)
{
scoreSystem[0] = 1;
scoreSystem[1] = -1;
scoreSystem[2] = -2;
}
else if (countNoGaps.Checked)
{
scoreSystem[0] = 1;
scoreSystem[1] = -1;
scoreSystem[2] = 0;
}
else
{
// gap options not selected
results.Text = "Please select if this alignment should count gaps or not" + "\r\n";
return;
}
ScoringMatrix simon = new ScoringMatrix(first, second, scoreSystem);
OptimumMatrix jack = new OptimumMatrix(first, second);
if (isGlobal.Checked)
{
for (int i = 1; i < first.Length; i++)
{
for (int j = 1; j < second.Length; j++)
{
jack.setScore(i, j, simon.calcCell(i, j));
}
}
}
else if (isLocal.Checked)
{
for (int i = 1; i < first.Length; i++)
{
for (int j = 1; j < second.Length; j++)
{
jack.setScore(i, j, simon.calcCellLocal(i, j));
}
}
}
else
{
// alignment type options not selected
results.Text = "Please select if this alignment should be global or local" + "\r\n";
return;
}
int[] maxPos = simon.getMaxScorePos();
string[] paul = jack.calcOptPathFrom(maxPos[0], maxPos[1]);
results.Text += paul[0] + "\r\n" + paul[1] + "\r\n\r\n";
}
static void Main(string[] args)
{
char[] first = { '-', 'A', 'G', 'C' };
char[] second = { '-', 'A', 'A', 'A', 'C' };
ScoringMatrix simon = new ScoringMatrix(first,second);
OptimumMatrix jack = new OptimumMatrix(first, second);
for (int i = 1; i < first.Length; i++)
{
for (int j = 1; j < second.Length; j++)
{
jack.setScore(i, j, simon.calcCell(i, j));
}
}
int[] maxPos = simon.getMaxScorePos();
string[] paul = jack.calcOptPathFrom(maxPos[0],maxPos[1]);
Console.WriteLine(paul[0]);
Console.WriteLine(paul[1]);
}
static void Main(string[] args)
{
char[] first = { '-', 'A', 'G', 'C' };
char[] second = { '-', 'A', 'A', 'A', 'C' };
ScoringMatrix simon = new ScoringMatrix(first, second);
OptimumMatrix jack = new OptimumMatrix(first, second);
for (int i = 1; i < first.Length; i++)
{
for (int j = 1; j < second.Length; j++)
{
jack.setScore(i, j, simon.calcCell(i, j));
}
}
int[] maxPos = simon.getMaxScorePos();
string[] paul = jack.calcOptPathFrom(maxPos[0], maxPos[1]);
Console.WriteLine(paul[0]);
Console.WriteLine(paul[1]);
}
