private void btnReset_Click(object sender, EventArgs e)
{
if (ccb_Added.Items.Count != 0)
{
mz_id_to_process.Clear();
ccb_Added.Items.Clear();
R_matrix.refresh();
update_figure(threshold);
}
}
public void save_data()
{
try
{
string fileNameofNet = file;
string data_name = String.Format("{0}\\{1}_{2}_{3}_{4}.txt", Path.GetDirectoryName(file),
Path.GetFileNameWithoutExtension(file),
X.ToString(),
Y.ToString(),
DateTime.Now.ToString("yyyy_MM_dd_HH_mm_ss"));
using (StreamWriter file_stream = new StreamWriter(data_name))
{
file_stream.WriteLine("selected X and Y");
file_stream.WriteLine("{0}\t{1}", X.ToString(), Y.ToString());
file_stream.WriteLine("X selected file");
file_stream.WriteLine(scanNamesListSelected[X] + " — " + sampleScanListSelected[X]);
file_stream.WriteLine("Y selected file");
file_stream.WriteLine(scanNamesListSelected[Y] + " — " + sampleScanListSelected[Y]);
file_stream.WriteLine("Threshold value and outliers level");
file_stream.WriteLine("{0}\t{1}", threshold.ToString(), threshold_outliers.ToString());
file_stream.WriteLine("m/z array values");
file_stream.WriteLine(R_matrix.mz_array.ToString <double>().Replace(' ', '\t'));
file_stream.WriteLine("scan X included values");
file_stream.WriteLine(R_matrix.scan(X).Multiply(mz_id_to_process).ToString <double>().Replace(' ', '\t'));
file_stream.WriteLine("scan X excluded values");
file_stream.WriteLine(R_matrix.scan(X).Multiply(mz_id_to_process.Multiply(-1).Add(1)).ToString <double>().Replace(' ', '\t'));
file_stream.WriteLine("scan Y included values");
file_stream.WriteLine(R_matrix.scan(Y).Multiply(mz_id_to_process).ToString <double>().Replace(' ', '\t'));
file_stream.WriteLine("scan Y excluded values");
file_stream.WriteLine(R_matrix.scan(Y).Multiply(mz_id_to_process.Multiply(-1).Add(1)).ToString <double>().Replace(' ', '\t'));
file_stream.WriteLine("Similarity matrix");
for (int i = 0; i < R_matrix.matrix.Rows(); i++)
{
file_stream.WriteLine(R_matrix.matrix.GetRow(i).ToString <double>().Replace(' ', '\t'));
}
file_stream.Close();
}
}
catch (Exception)
{ }
}
public void clicked_pixel(int X, int Y)
{
picture_R.Refresh();
GraphPane plot1 = master.PaneList[0];
GraphPane plot2 = master.PaneList[1];
plot1.CurveList.Clear();
plot2.CurveList.Clear();
plot1.YAxis.Scale.Min = 0;
plot2.YAxis.Scale.Min = 0;
LineItem myCurve1 = plot1.AddCurve("Included in calculations", R_matrix.mz_array, R_matrix.scan(Y).Multiply(mz_id_to_process.Add(-0.5).Multiply(2)), Color.Blue, SymbolType.None);
LineItem myCurve2 = plot2.AddCurve("", R_matrix.mz_array, R_matrix.scan(X).Multiply(mz_id_to_process.Add(-0.5).Multiply(2)), Color.Blue, SymbolType.None);
LineItem myCurve3 = plot1.AddCurve("Excluded from calculations", R_matrix.mz_array, R_matrix.scan(Y).Multiply(mz_id_to_process.Add(-0.5).Multiply(-2)), Color.Red, SymbolType.None);
LineItem myCurve4 = plot2.AddCurve("", R_matrix.mz_array, R_matrix.scan(X).Multiply(mz_id_to_process.Add(-0.5).Multiply(-2)), Color.Red, SymbolType.None);
plot1.Legend.Position = LegendPos.Float;
plot1.Legend.Location.CoordinateFrame = CoordType.ChartFraction;
plot1.Legend.Location.AlignH = AlignH.Right;
plot1.Legend.Location.AlignV = AlignV.Top;
plot1.Legend.Location.TopLeft = new PointF(1.0f - 0.02f, 0.02f);
plot1.XAxis.Title.FontSpec.Size = 20.0f;
plot2.XAxis.Title.FontSpec.Size = 20.0f;
plot1.YAxis.Title.FontSpec.Size = 20.0f;
plot2.YAxis.Title.FontSpec.Size = 20.0f;
plot1.Title.FontSpec.Size = 20.0f;
plot2.Title.FontSpec.Size = 20.0f;
plot1.XAxis.Title.Text = "m/z, Th";
plot2.XAxis.Title.Text = "m/z, Th";
plot1.YAxis.Title.Text = "intensity";
plot2.YAxis.Title.Text = "intensity";
plot1.Title.Text = scanNamesListSelected[Y] + " — " + sampleScanListSelected[Y];
plot2.Title.Text = scanNamesListSelected[X] + " — " + sampleScanListSelected[X];
labelR.Text = "R=" + (R_matrix.matrix[X, Y]).ToString();
zgc.AxisChange();
zgc.Invalidate();
zgc.Refresh();
}
public void update_ccbox()
{
ccb_Added.Items.Clear();
int st_inc = 0;
int st_exc = 0;
if (mz_id_to_process.Sum() > 0 && mz_id_to_process.Sum() < R_matrix.mz_array.Length)
{
for (int i = 1; i < mz_id_to_process.Length; i++)
{
if (mz_id_to_process[i] != mz_id_to_process[i - 1])
{
if (mz_id_to_process[i - 1] == 0)
{
CCBoxItem item = new CCBoxItem(R_matrix.mz_array[st_exc], R_matrix.mz_array[i - 1], false);
ccb_Added.Items.Add(item);
st_inc = i;
}
else
{
CCBoxItem item = new CCBoxItem(R_matrix.mz_array[st_inc], R_matrix.mz_array[i - 1], true);
ccb_Added.Items.Add(item);
st_exc = i;
}
}
}
if (mz_id_to_process[mz_id_to_process.Length - 1] == 0)
{
CCBoxItem item = new CCBoxItem(R_matrix.mz_array[st_exc], R_matrix.mz_array[mz_id_to_process.Length - 1], false);
ccb_Added.Items.Add(item);
}
else
{
CCBoxItem item = new CCBoxItem(R_matrix.mz_array[st_inc], R_matrix.mz_array[mz_id_to_process.Length - 1], true);
ccb_Added.Items.Add(item);
}
}
else
{
R_matrix.refresh();
}
}
public void read_r_matrix(string fileName)
{
try
{
//var mzxml = new LIMPFileReader.LimpXml(fileName, (float)0, true);
Cursor = Cursors.WaitCursor;
var reader = new MatReader(fileName);
var structure = reader["data"];
var cType = structure["spectra"].ValueType;
var fields = structure.Fields;
//var scans = (reader["result"]["scans"].GetValue<int[,]>()).ToDouble();
var scans = reader["data"]["spectra"].GetValue <double[, ]>().Transpose();
R_matrix.mz_array = reader["data"]["mz"].GetValue <double[, ]>().ToJagged()[0];
mzmin = R_matrix.mz_array[0];
mzmax = R_matrix.mz_array[R_matrix.mz_array.Length - 1];
n_precision = (int)(Math.Round(1.0 / (R_matrix.mz_array[1] - R_matrix.mz_array[0])));
rf = new double[scans.Columns(), scans.Columns()];
R_matrix.matrix = rf;
rf2 = new double[rf.Columns(), rf.Rows()];
R_matrix.scans = scans.Transpose();
int mzlength = scans.GetLength(0);
var scannames = reader["data"]["filenames"];
var scan_of_file = (reader["data"]["scan_of_file"].GetValue <double[, ]>()).ToInt32();
scannames_count = scan_of_file.Length;
sampleNameList.Clear();
sampleNameList.Add(scannames[scan_of_file[0, 0]].Value.ToString());
sampleCoordList.Clear();
sampleCoordList.Add(0.0);
scanNamesList.Clear();
int intercept = 0;
for (int i = 0; i < scannames_count; i++)
{
scanNamesList.Add(scannames[scan_of_file[0, i]].Value.ToString());
if (i > 0)
{
if (scannames[scan_of_file[0, i]].Value.ToString() != scannames[scan_of_file[0, i - 1]].Value.ToString())
{
sampleNameList.Add(scannames[scan_of_file[0, i]].Value.ToString());
sampleCoordList.Add(i);
intercept = i;
}
}
sampleScanList.Add(Convert.ToString(i + 1 - intercept));
}
R_matrix.scan_names = sampleScanList;
R_matrix.file_names = sampleNameList;
R_matrix.refresh();
update_figure(threshold);
Cursor = Cursors.Arrow;
}
catch (Exception e)
{
var msg = e.Message;
Cursor = Cursors.Arrow;
MessageBox.Show(msg, "Warning", MessageBoxButtons.OK, MessageBoxIcon.Information, MessageBoxDefaultButton.Button1, MessageBoxOptions.DefaultDesktopOnly);
return;
}
}
