/// <summary>
/// Get the spectra from the new quantification.
/// </summary>
/// <param name="result">The quantification result.</param>
private void GetSpectra(QuantResult result)
{
// Get the cit spectrum ID
int citSpectrumId = result.CitSpectrumID;
// From the validation type, get the spectra information
if (result.ValidationBy == "Cit-paired")
{
// Loop through all of the cit spectra to get the spectra
foreach (var item in Quantification.citSpecSpecDict)
{
if (item.Key.ID == citSpectrumId)
{
citSpectrum = item.Key;
argSpectrum = item.Value;
}
}
}
else
{
// Loop through all of the arg spectra to get the spectra
foreach (var item in Quantification.argSpecScanDict)
{
if (item.Value.ScanNumber == citSpectrumId)
{
citSpectrum = item.Value;
argSpectrum = item.Key;
}
}
}
}
/// <summary>
/// Get the spectra from the new quantification.
/// </summary>
/// <param name="result">The quantification result.</param>
private void GetSpectra(QuantResult result)
{
// Get the cit spectrum ID
int citSpectrumId = result.CitSpectrumID;
foreach (var item in Quantification.loneCitSpecList)
{
if (item.ID == citSpectrumId)
{
citSpectrum = item;
}
}
}
/// <summary>
/// Quantification of citrullinations.
/// </summary>
/// <param name="resultsQuant">The list of quantification results.</param>
private static void CitrullinationQuantification(List <QuantResult> resultsQuant)
{
// Loop through each of the citrullinted spectra
foreach (KeyValuePair <XTSpectrum, XTSpectrum> kvp in citSpecSpecDict)
{
// Create an empty instance of quantification result
QuantResult result = new QuantResult();
// Create two temporary variables for holding the extracted ion count for both citrulline and arginine
double citXIC = 0;
double argXIC = 0;
// Loop through the input files and find the one that have the same input filename
foreach (Input input in FileReader.inputFiles)
{
string inputFileName = input.FilePath.Split('\\').Last();
if (inputFileName == kvp.Key.OriginalFileName)
{
citXIC = CalculateExtractedIonCount(kvp.Key, citXIC, input);
}
if (inputFileName == kvp.Value.OriginalFileName)
{
argXIC = CalculateExtractedIonCount(kvp.Value, argXIC, input);
}
}
// Add the data to the quantification result
result.Protein = RemoveProteinDbPrefix(kvp.Key.Proteins[0].ProtLabel);
result.Sequence = kvp.Key.Proteins[0].DoaminSeq;
result.CitrullinatedExtractedIonCount = citXIC;
result.ArginineExtractedIonCount = argXIC;
result.CitPercent = citXIC / (citXIC + argXIC) * 100;
result.ValidationBy = "Cit-paired";
result.CitFileName = kvp.Key.OriginalFileName;
result.ArgFileName = kvp.Value.OriginalFileName;
result.CitRetentionTime = kvp.Key.RetentionTime;
result.ArgRetentionTime = kvp.Value.RetentionTime;
result.CitCharge = kvp.Key.Charge;
result.ArgCharge = kvp.Value.Charge;
result.CitSpectrumID = kvp.Key.ID;
result.ArgSpectrumID = kvp.Value.ID;
result.Score = kvp.Key.CitScore;
result.MatchScore = kvp.Value.MatchScore;
// Add the result to the result list
resultsQuant.Add(result);
}
}
/// <summary>
/// Update the window
/// </summary>
/// <param name="result"></param>
internal void UpdateWindow(QuantResult result)
{
_result = result;
GetSpectra(_result);
SetCitInfo();
ValidationUIUtilities.ClearChart(chartMS1);
ValidationUIUtilities.ClearChart(chartMS2);
ValidationUIUtilities.CreateMS1Chart(chartMS1, citSpectrum);
ValidationUIUtilities.CreateLoneCitMs2Chart(chartMS2, citSpectrum);
ValidationUIUtilities.FillIonGridGeneral(metroGridCitIons, citSpectrum, HelperUtilities.CreateAAArray(_result.Sequence));
if (Quantification.QuantificationResults.Contains(result))
{
metroButtonAddQuant.Enabled = false;
metroButtonRemoveQuant.Enabled = true;
}
else
{
metroButtonAddQuant.Enabled = true;
metroButtonRemoveQuant.Enabled = false;
}
}
/// <summary>
/// Quantification of lonely citrullinations.
/// </summary>
/// <param name="resultsQuant">The list of quantification results.</param>
private static void LoneCitrullinationQunatification(List <QuantResult> resultsQuant)
{
// Loop through all of the lonely citrullination spectra
foreach (XTSpectrum spectrum in loneCitSpecList)
{
// Create an empty instance of quantification result
QuantResult result = new QuantResult();
// Calculate the extracted ion count for the spectrum
// Create a placeholder variable for the extracted ion count
double citXIC = 0;
// Loop through the input files and find the one that have the same input filename
foreach (Input input in FileReader.inputFiles)
{
string inputFileName = input.FilePath.Split('\\').Last();
if (inputFileName == spectrum.OriginalFileName)
{
citXIC = CalculateExtractedIonCount(spectrum, citXIC, input);
}
}
// Add the data to the quantification result
result.Protein = RemoveProteinDbPrefix(spectrum.Proteins[0].ProtLabel);
result.Sequence = spectrum.Proteins[0].DoaminSeq;
result.CitrullinatedExtractedIonCount = citXIC;
result.ArginineExtractedIonCount = 0;
result.CitPercent = 100;
result.ValidationBy = "Lone";
result.CitFileName = spectrum.OriginalFileName;
result.CitRetentionTime = spectrum.RetentionTime;
result.ArgFileName = "NaN";
result.ArgRetentionTime = 0;
result.CitCharge = spectrum.Charge;
result.ArgCharge = 0;
result.ArgSpectrumID = 0;
result.CitSpectrumID = spectrum.ID;
result.Score = spectrum.CitScore;
result.MatchScore = 0;
// Add the result to the result list
resultsQuant.Add(result);
}
}
/// <summary>
/// Update the quantification window.
/// </summary>
/// <param name="result">The quantification result.</param>
internal void UpdateWindow(QuantResult result)
{
// Set the result
_result = result;
// Get the spectra
GetSpectra(_result);
// Add the info
SetCitInfo();
SetArgInfo();
// Clear the charts
ValidationUIUtilities.ClearChart(chartArgMS1);
ValidationUIUtilities.ClearChart(chartCitMS1);
ValidationUIUtilities.ClearChart(chartMS2);
// Create the charts
ValidationUIUtilities.CreateMS1Chart(chartArgMS1, argSpectrum);
ValidationUIUtilities.CreateMS1Chart(chartCitMS1, citSpectrum);
ValidationUIUtilities.CreatePairedMs2Chart(chartMS2, citSpectrum, argSpectrum);
// Create the ion grid
ValidationUIUtilities.FillIonGridGeneral(metroGridArgIons, argSpectrum, HelperUtilities.CreateAAArray(_result.Sequence));
ValidationUIUtilities.FillIonGridGeneral(metroGridCitIons, citSpectrum, HelperUtilities.CreateAAArray(_result.Sequence));
// Set the title and spectrum ID
labelTitel.Text = string.Format("Quantification - Paired (By {0})", _result.ValidationBy);
metroLabelCitSpectrumID.Text = _result.CitSpectrumID.ToString();
metroLabelArgSpectrumID.Text = _result.ArgSpectrumID.ToString();
if (Quantification.QuantificationResults.Contains(result))
{
metroButtonAddQuant.Enabled = false;
metroButtonRemoveQuant.Enabled = true;
}
else
{
metroButtonAddQuant.Enabled = true;
metroButtonRemoveQuant.Enabled = false;
}
}
/// <summary>
/// Create a new instance of <see cref="QuantificationLone"/>.
/// </summary>
/// <param name="result">The quantification result.</param>
internal QuantificationLone(QuantResult result)
{
InitializeComponent();
UpdateWindow(result);
}
