private void ReverseComplement(RichTextBox textBoxToReverseComplement)
{
textBoxToReverseComplement.Enabled = false;
char[] charArray = textBoxToReverseComplement.Text.ToCharArray();
Array.Reverse(charArray);
textBoxToReverseComplement.Enabled = true;
this.ActiveControl = textBoxToReverseComplement;
textBoxToReverseComplement.Text = DataFunctions.ReturnComplement(charArray);
textBoxToReverseComplement.Select(textBoxToReverseComplement.Text.Length, 0);
}
private void findSubsequenceButton_Click(object sender, EventArgs e)
{
int permitedMismatchCount = (int)this.mismatchCounter.Value;
bool searchComplement = this.complementCheckbox.Checked;
bool searchReverseComplement = this.reverseComplementCheckbox.Checked;
/// Just in case
string inputFromFindBox = string.Join("", this.searchTextBox.Text.Split(new[] { " ", "\r\n", "\r", "\n", Environment.NewLine }, StringSplitOptions.RemoveEmptyEntries)).ToUpper();
string sequence = this.rtb.Text.ToUpper();
int subsequenceLength = inputFromFindBox.Length;
Dictionary <int, int> foundPositions = new Dictionary <int, int>();
List <string> subsequencesToSearch = new List <string>();
subsequencesToSearch.Add(inputFromFindBox);
if (searchComplement)
{
subsequencesToSearch.Add(DataFunctions.ReturnComplement(inputFromFindBox));
}
if (searchReverseComplement)
{
char[] charSubsequence = inputFromFindBox.ToCharArray();
Array.Reverse(charSubsequence);
subsequencesToSearch.Add(DataFunctions.ReturnComplement(charSubsequence));
}
for (int i = 0; i < sequence.Length - subsequenceLength + 1; i++)
{
foreach (string searchSubstring in subsequencesToSearch)
{
int currentCycleMismatchCount = 0;
for (int j = 0; j < subsequenceLength; j++)
{
if (searchSubstring[j] == sequence[i + j] || searchSubstring[j] == 'N' || sequence[i + j] == 'N')
{
continue;
}
else
{
currentCycleMismatchCount++;
}
}
if (currentCycleMismatchCount > permitedMismatchCount)
{
continue;
}
else
{
foundPositions.Add(i, i + subsequenceLength);
}
}
}
foreach (KeyValuePair <int, int> positions in foundPositions)
{
int beginning = positions.Key;
int end = positions.Value;
int rtbTextLength = this.rtb.Text.Length;
//Check in case the content of textbox has changed (in this case the results may be invalid anyway)
if (beginning >= rtbTextLength || end > rtbTextLength)
{
continue;
}
rtb.Select(beginning, (end - beginning));
rtb.SelectionColor = System.Drawing.Color.Yellow;
rtb.SelectionBackColor = System.Drawing.Color.Black;
}
rtb.Select(rtb.Text.Length, 0);
rtb.SelectionColor = Color.Black;
rtb.SelectionBackColor = Color.White;
}
