/// <summary>
/// Update the validation window with a new spectrum
/// </summary>
/// <param name="argSpectrumValID">The new spectrum ID.</param>
internal void UpdateValidationArgUI(int argSpectrumValID)
{
// Get the spectrum
FindArginineSpectraKeyValuePair(argSpectrumValID);
// If the spectra is marked for quantification, get the index of the complementary spectra that has been marked
int complIndex = 0;
if (Validation.argChosenForQuantList.Contains(valKVP.Key.ID))
{
complIndex = Quantification.GetQuantifiedComplementaryCitSpectrumIndex(valKVP.Key, valKVP.Value);
}
// Update the spectrum ID label
ChangeSpectrumIDAndScoreLabel();
// Clear the chart
ValidationUIUtilities.ClearChart(chartMS2);
// Create the chart
ValidationUIUtilities.CreatePairedMs2Chart(chartMS2, valKVP.Value[complIndex], valKVP.Key);
ValidationUIUtilities.ClearChart(chartArgMS1);
ValidationUIUtilities.ClearChart(chartPotCitMS1);
// Update the MS1 charts
ValidationUIUtilities.CreateMS1Chart(chartArgMS1, valKVP.Key);
ValidationUIUtilities.CreateMS1Chart(chartPotCitMS1, valKVP.Value[complIndex]);
// Fill the ion grid with data
ValidationUIUtilities.FillCitIonGrid(metroGridArgIons, valKVP.Key);
ValidationUIUtilities.FillArgIonGrid(metroGridPotCitIons, valKVP.Value[complIndex], valKVP.Key);
// Check if buttons should be enabled or disabled
CheckBeforeButtonDisabling();
EnableQuantButtons(valKVP.Key);
ReturnPotCitIndex(complIndex);
// Add information about peptides
AddArgInfo();
AddPotCitInfo(complIndex);
}
/// <summary>
/// Update the spectrum validation.
/// </summary>
/// <param name="spectrumValID">The spectrum ID.</param>
internal void UpdateValidationUI(int spectrumValID)
{
// Find the citrullinated spectrum
FindCitrullineSpectraKeyValuePair(spectrumValID);
// If the spectra is marked for quantification, get the index of the complementary spectra that has been marked
int complIndex = 0;
if (Validation.citChosenForQuantList.Contains(valKVP.Key.ID))
{
complIndex = Quantification.GetQuantifiedComplementaryArgSpectrumId(valKVP.Key, valKVP.Value);
}
// Update the spectrum id label
ChangeSpectrumIDAndScoreLabel();
// Update the MS2 chart
ValidationUIUtilities.ClearChart(chartMS2);
ValidationUIUtilities.CreatePairedMs2Chart(chartMS2, valKVP.Key, valKVP.Value[complIndex]);
// Update the MS1 charts
ValidationUIUtilities.ClearChart(chartCitMS1);
ValidationUIUtilities.ClearChart(chartArgMS1);
ValidationUIUtilities.CreateMS1Chart(chartCitMS1, valKVP.Key);
ValidationUIUtilities.CreateMS1Chart(chartArgMS1, valKVP.Value[complIndex]);
// Update the ion grid
ValidationUIUtilities.FillCitIonGrid(metroGridCitIons, valKVP.Key);
ValidationUIUtilities.FillCitIonGrid(metroGridArgIons, valKVP.Value[complIndex]);
// Update the buttons
CheckBeforeButtonDisabling();
EnableQuantButtons(valKVP.Key);
ReturnArgIndex(complIndex);
// Update the information
AddCitInfo();
AddArgInfo(complIndex);
}
/// <summary>
/// Remove the spectrum from quantification.
/// </summary>
private void MetroButtonRemoveQuant_Click(object sender, EventArgs e)
{
// Remove the spectrum from the dictionary
Quantification.RemoveFromkvpArgSpecScanDict(valKVP.Key);
// Update the quantification id list
UpdateChosenForQuant(valKVP.Key.ID, false);
// Enable and disable the button
// Enable moving back and forth through the complementary spectra
metroButtonNextPotCitScan.Enabled = true;
metroButtonPrevPotCitScan.Enabled = true;
// Check if has reached the end
int length = valKVP.Value.Count() - 1;
int index = potCitIndex + 1;
if (index > length)
{
// If so, disable the next button
metroButtonNextPotCitScan.Enabled = false;
}
//Check if has reached the start
int index1 = potCitIndex - 1;
if (index1 < 0)
{
// If so, disable the previous button
metroButtonPrevPotCitScan.Enabled = false;
}
// Disable the remove button and enable the add button
metroButtonRemoveQuant.Enabled = false;
metroButtonAddQuant.Enabled = true;
}
/// <summary>
/// Remove the spectrum from quantification.
/// </summary>
private void MetroButtonRemoveQuant_Click(object sender, EventArgs e)
{
// Remove the spectrum from the dictionary
Quantification.RemoveFromLoneCitSpecList(valSpec);
// Update the quantification id list
UpdateChosenForQuant(valSpec.ID, false);
// Enable and disable the button
metroButtonRemoveQuant.Enabled = false;
metroButtonAddQuant.Enabled = true;
}
/// <summary>
/// Add the spectrum to quantification.
/// </summary>
private void MetroButtonAddQuant_Click(object sender, EventArgs e)
{
// Get the spectrum
XTSpectrum spectrumCit = valSpec;
// Add the spectrum to the dictionary
Quantification.AddToLoneCitSpecList(spectrumCit);
// Update the quantification id list
UpdateChosenForQuant(valSpec.ID, true);
// Enable and disable the button
metroButtonAddQuant.Enabled = false;
metroButtonRemoveQuant.Enabled = true;
}
/// <summary>
/// Add the Lone Cit Spectra to quantification.
/// </summary>
/// <param name="scoredSpectra">The spectra to be added.</param>
private static void AddLoneCitSpectraAboveCutoffToQunatification(List <XTSpectrum> scoredSpectra)
{
// Loop through the spectra
foreach (XTSpectrum spectrum in scoredSpectra)
{
// Check that the CitScore is greater than the CutOff value
if (spectrum.CitScore >= ScoreSettings.CutOffScore)
{
// If the spectrum passes, add the spectrum to the quantification
Quantification.AddToLoneCitSpecList(spectrum);
Validation.loneCitChosenForQuantList.Add(spectrum.ID);
}
}
}
/// <summary>
/// Add the spectrum to quantification.
/// </summary>
private void MetroButtonAddQuant_Click(object sender, EventArgs e)
{
// Add the spectrum to the dictionary
Quantification.AddTokvpArgSpecScanDict(valKVP.Key, valKVP.Value[potCitIndex]);
// Update the quantification id list
UpdateChosenForQuant(valKVP.Key.ID, true);
// Enable and disable the button
// Prevent moving back and forth through the complementary spectra
metroButtonNextPotCitScan.Enabled = false;
metroButtonPrevPotCitScan.Enabled = false;
// Enable the remove button and disable the add button
metroButtonAddQuant.Enabled = false;
metroButtonRemoveQuant.Enabled = true;
}
/// <summary>
/// Add the Cit Spectra to quantification.
/// </summary>
/// <param name="scoredSpectra">The spectra to be added.</param>
private static void AddCitSpectraAboveCutoffToQuantification(Dictionary <XTSpectrum, List <XTSpectrum> > scoredSpectra)
{
// Loop through all of the spectra
foreach (KeyValuePair <XTSpectrum, List <XTSpectrum> > spectrum in scoredSpectra)
{
// Check that the CitScore is greater than the CutOff value
if (spectrum.Key.CitScore >= ScoreSettings.CutOffScore)
{
// If the spectrum passes, add the spectrum to the quantification together with the complementary spectrum with the highest match score
Quantification.AddTokvpCitSpecSpecDict(spectrum.Key, spectrum.Value[0]);
// Add the spectrum ID to the list
Validation.citChosenForQuantList.Add(spectrum.Key.ID);
}
}
}
/// <summary>
/// Add the spectrum to quantification.
/// </summary>
private void MetroButtonAddQuant_Click(object sender, EventArgs e)
{
// Get the spectra
XTSpectrum spectrumCit = valKVP.Key;
XTSpectrum spectrumArg = valKVP.Value[argIndex];
// Add the spectrum to the dictionary
Quantification.AddTokvpCitSpecSpecDict(spectrumCit, spectrumArg);
// Update the quantification id list
UpdateChosenForQuant(valKVP.Key.ID, true);
// Prevent moving back and forth through the complementary spectra
metroButtonNextArgScan.Enabled = false;
metroButtonPrevArgScan.Enabled = false;
// Enable and disable the button
metroButtonAddQuant.Enabled = false;
metroButtonRemoveQuant.Enabled = true;
}
/// <summary>
/// Add the Arg Spectra to quantification.
/// </summary>
/// <param name="scoredSpectra">The spectra to be added.</param>
private static void AddArgSpectraAboveCutOffToQuantification(Dictionary <XTSpectrum, List <RawScan> > scoredSpectra)
{
// Loop through all of the spectra
foreach (KeyValuePair <XTSpectrum, List <RawScan> > spectrum in scoredSpectra)
{
// Loop through all of the complementary cit spectra
foreach (RawScan complSpectra in spectrum.Value)
{
// Check that the CitScore is greater than the CutOff value
if (complSpectra.CitScore >= ScoreSettings.CutOffScore && Quantification.argSpecScanDict.ContainsKey(spectrum.Key) == false)
{
// If the spectrum passes, add the spectrum to the quantification together with the arginine spectra
Quantification.AddTokvpArgSpecScanDict(spectrum.Key, complSpectra);
Validation.argChosenForQuantList.Add(spectrum.Key.ID);
}
}
}
}