private void AddNewMols_Click(object sender, EventArgs e)
{
var stopWatch = new Stopwatch();
stopWatch.Start();
string xmapFilePath = XMAP_path_txtbox.Text;
string bnxFilePath = BNX_path_txtbox.Text;
string[] runRootDirs = runs_paths_txtbx.Text.Split('\n');
int alignmentLabelChannel = int.Parse(mol_upload_alignment_ch_txtbx.Text);
if (String.IsNullOrEmpty(xmapFilePath))
{
MessageBox.Show("Must provide path to XMAP file", "Missing file path");
return;
}
if (String.IsNullOrEmpty(bnxFilePath))
{
MessageBox.Show("Must provide path to BNX file", "Missing file path");
return;
}
if (String.IsNullOrEmpty(runRootDirs[0]))
{
MessageBox.Show("Must provide path to root directory of run files", "Missing file path");
return;
}
int totalALignedMolecules = XMAPParser.ParseXmap(xmapFilePath);
if (totalALignedMolecules == -1)
{
MessageBox.Show("Can't open specified XMAP file", "Error opening file");
return;
}
int totalMolecules = BNXParser.ParseBNX(bnxFilePath, projectID, alignmentLabelChannel, runRootDirs);
if (totalMolecules == -1)
{
MessageBox.Show("Can't open specified BNX file", "Error opening file");
return;
}
MessageBox.Show(String.Format("time elapsed: {0}", stopWatch.Elapsed.ToString()));
XMAPParser.moleculeData.Clear();
}
public static void FitMoleculeToRef(Molecule molecule, bool saveChannel1Intensities, bool saveChannel2Intensities, string outputDir)
{
List <Tuple <int, int> > labelIdAlignmentPositions = XMAPParser.ParseAlignmentString(molecule.AlignmentString); //in each tuple item1 = ref, item2 = molecule
string[] molAlignmentLabelPositions = molecule.AlignmentChannelLabelPositions.Split('\t');
List <double> refPositions = new List <double>();
List <double> molPositions = new List <double>();
//Dictionary<int, double> molFitPixelPositions = new Dictionary<int, double>();
double currRefPosition, currMolPosition;
foreach (Tuple <int, int> labelIdAlignment in labelIdAlignmentPositions)
{
currRefPosition = rCmapPositions[molecule.ChromId][labelIdAlignment.Item1 - 1]; //position along chromosome in bp
currMolPosition = double.Parse(molAlignmentLabelPositions[labelIdAlignment.Item2 - 1]) / bpPerPixel; //position along molecule in pixels
if (!refPositions.Contains(currRefPosition) && !molPositions.Contains(currMolPosition))
{
refPositions.Add(currRefPosition);
molPositions.Add(currMolPosition);
}
}
if (molecule.Orientation == "-")
{
refPositions.Reverse();
molPositions.Reverse();
}
IInterpolation linearInterpolation = Interpolate.Linear(molPositions, refPositions);
if (saveChannel1Intensities)
{
SaveMoleculePixelsToFile(linearInterpolation, molecule, 1, outputDir);
}
if (saveChannel2Intensities)
{
SaveMoleculePixelsToFile(linearInterpolation, molecule, 2, outputDir);
}
}
