public ProtQuant(FastaItem fi, PepQuant pq)
{
MyFastaItem = fi;
MyPepQuants = new List <PepQuant>()
{
pq
};
}
private void ShowPeptideWindow(Dictionary <string, object> ao)
{
PlotModel MyModel = new PlotModel();
PepQuant sc = MyPeptides.Find(a => a.Sequence.Equals(ao["Sequence"]));
//ObservableCollection<MyDataPoint> BarChartData = new ObservableCollection<MyDataPoint>();
SignalViewer ws = new SignalViewer();
ws.Title = "Peptide: " + sc.Sequence;
MyModel.Title = sc.Sequence;
// --------------------------------------------------------------------------------------------------------
MyModel.Title = sc.Sequence;
MyModel.LegendOrientation = LegendOrientation.Horizontal;
MyModel.LegendPlacement = LegendPlacement.Outside;
MyModel.LegendPosition = LegendPosition.BottomCenter;
DataTable dtDataGridView = new DataTable("PepScans");
DataSet dataSetBarChart = new DataSet();
DataTable dtBarChart = new DataTable("PepScans");
dataSetBarChart.Tables.Add(dtBarChart);
dtBarChart.Columns.Add("channel", typeof(string));
dtDataGridView.Columns.Add("File Name", typeof(string));
dtDataGridView.Columns.Add("Precursor Charge", typeof(int));
dtDataGridView.Columns.Add("Scan Number", typeof(int));
List <DataRow> dataRowBarChartList = new List <DataRow>();
var categoryAxis = new CategoryAxis();
var valueAxis = new LinearAxis();
valueAxis.Title = "Intensity";
valueAxis.Position = AxisPosition.Left;
MyModel.Axes.Add(valueAxis);
for (int i = 0; i < sc.MyQuants[0].MarkerIntensities.Count; i++)
{
if (classLabels[i] >= 0)
{
DataRow newRowBarChart = dtBarChart.NewRow();
newRowBarChart["channel"] = "Channel " + (i + 1);
dataRowBarChartList.Add(newRowBarChart);
dtBarChart.Rows.Add(newRowBarChart);
dtDataGridView.Columns.Add(new DataColumn("Channel " + (i + 1).ToString(), typeof(double)));
categoryAxis.Labels.Add(new DataColumn("Channel " + (i + 1).ToString(), typeof(double)).ToString());
}
}
MyModel.Axes.Add(categoryAxis);
bool insertYaxisBarChart = true;
int counter = 0;
List <int> categoryIndex = new List <int>();
List <double> value = new List <double>();
foreach (Quant q in sc.MyQuants)
{
if (insertYaxisBarChart)
{
// Set the Y-Axis value
for (int i = 0; i < sc.MyQuants.Count; i++)
{
dtBarChart.Columns.Add("spec" + i, typeof(double));
//ws.BarChart1.ValueField.Add("spec" + i);
categoryIndex.Add(i);
}
insertYaxisBarChart = false;
}
DataRow newRow_datagridview = dtDataGridView.NewRow();
newRow_datagridview["File Name"] = q.FileName;
newRow_datagridview["Scan Number"] = q.ScanNumber;
newRow_datagridview["Precursor Charge"] = q.Z;
var columnSeries = new ColumnSeries();
columnSeries.Title = q.FileName;
int negativeClass = 0;
var solution = classLabels.GroupBy(i => i > 0).SelectMany(g => g).ToArray();
//classLabels.Sort((a, b) => b.CompareTo(a));
for (int i = 0; i < q.MarkerIntensities.Count; i++)
{
if (classLabels[i] >= 0)
{
DataRow newRow_barChart = dataRowBarChartList[i - negativeClass];
newRow_barChart["spec" + counter] = q.MarkerIntensities[i];
newRow_datagridview[i + 3 - negativeClass] = q.MarkerIntensities[i];
//BarChartData.Add(new MyDataPoint(i, q.MarkerIntensities[i], "Row" + " " + counter));
columnSeries.Items.Add(new ColumnItem(q.MarkerIntensities[i], (i - negativeClass)));
}
else
{
negativeClass++;
}
}
counter++;
MyModel.Series.Add(columnSeries);
dtDataGridView.Rows.Add(newRow_datagridview);
}
// Set the chart tooltip. {field} will be replaced by current bar value.
// Need to improve in this little templating.
//ws.BarChart1.ToolTipText = "Signal Intensity: {field}";
// Set the x-axis data field
//ws.BarChart1.XAxisField = "channel";
//--------------------------------------------------------------------------------------------------------
//ws.MyBarChart.HorizontalPropertyName = "X";
//ws.BarChart1.DataSource = dataSetBarChart;
//ws.MyBarChart.Items = BarChartData;
//ws.BarChart1.Generate();
//ws.MyBarChart.Draw();
//ws.MyBarChart.Refresh();
ws.MyDataGridSpec.ItemsSource = dtDataGridView.DefaultView;
ws.Show();
ws.MyBarChart.Model = MyModel;
}
/// <summary>
///
/// </summary>
/// <param name="fileName"></param>
/// <param name="onlyUniquePeptides"></param>
/// <param name="classLabels"></param>
/// <param name="minQuantsPerPeptide"></param>
/// <returns>the list ofchannels and the list of peptides</returns>
///
public static KeyValuePair <List <FastaItem>, List <PepQuant> > ParsePeptideReport(string fileName)
{
List <PepQuant> pepsAll = new List <PepQuant>();
bool fastaData = false;
List <FastaItem> MyFastaItems = new List <FastaItem>();
List <PepQuant> peps = new List <PepQuant>();
StreamReader sr = new StreamReader(fileName);
string line;
int counter = 0;
PepQuant pq = null;
while ((line = sr.ReadLine()) != null)
{
counter++;
//Console.WriteLine("Parsing line: " + counter);
if (line.Equals("#Fasta Items"))
{
fastaData = true;
}
else if (line.StartsWith("#Channels"))
{
continue;
}
else if (fastaData)
{
//Parse fasta data
if (line.StartsWith(">"))
{
string[] cols = Regex.Split(line, " ");
string protID = cols[0].ToString();
protID = protID.Remove(0, 1);
string protDesc = "";
for (int i = 0; i < cols.Length; i++)
{
if (i == 0)
{
continue;
}
if (i == 1)
{
protDesc += cols[1];
}
else
{
protDesc += " " + cols[i];
}
}
FastaItem fi = new FastaItem(protID, protDesc);
MyFastaItems.Add(fi);
}
else
{
MyFastaItems.Last().Sequence += line;
}
}
else
{
if (line.StartsWith("Peptide:"))
{
peps.Add(pq);
string[] cols = Regex.Split(line, "\t");
//GetSequence
string[] colsSeq = Regex.Split(cols[0], ":");
pq = new PepQuant(colsSeq[1]);
}
else
{
//quant line
List <string> cols = Regex.Split(line, "\t").ToList();
List <string> cols2 = Regex.Split(cols[0], Regex.Escape(".")).ToList();
int scanNumber = int.Parse(cols2[cols2.Count - 2]);
int z = int.Parse(cols2.Last());
string filename = Regex.Replace(cols[0], Regex.Escape(".") + scanNumber + Regex.Escape(".") + scanNumber + Regex.Escape(".") + z, "");
//Get the signals
cols.RemoveAt(0);
try {
List <double> signals = cols.Select(a => double.Parse(a)).ToList();
//This fix is required because sometimes the purity correction may yield negative numbers.
for (int i = 0; i < signals.Count; i++)
{
if (signals[i] < 0)
{
signals[i] = 0;
}
}
int qc = signals.Count(a => a > 0);
if (!signals.Contains(double.NaN))
{
pq.MyQuants.Add(new Quant(z, filename, scanNumber, signals));
}
} catch
{
Console.WriteLine("Failed parsing line: " + counter);
}
}
}
}
peps.Add(pq);
peps.RemoveAt(0);
pepsAll.AddRange(peps);
sr.Close();
pepsAll.RemoveAll(a => a.MyQuants.Count == 0);
return(new KeyValuePair <List <FastaItem>, List <PepQuant> >(MyFastaItems, pepsAll));
}
