/// <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>
/// 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 spectrum
FindSpec(spectrumValID);
// Update the MS2 chart
ValidationUIUtilities.ClearChart(chartMS2);
ValidationUIUtilities.CreateLoneCitMs2Chart(chartMS2, valSpec);
// Update the MS1 chart
ValidationUIUtilities.ClearChart(chartMS1);
ValidationUIUtilities.CreateMS1Chart(chartMS1, valSpec);
// Fill the ion grid
ValidationUIUtilities.FillCitIonGrid(metroGridCitIons, valSpec);
// Update the quantification buttons.
EnableQuantButtons(valSpec);
// Add the citrullination information
AddCitInfo();
}
/// <summary>
/// Go to the previous arginine scan.
/// </summary>
private void MetroButtonPrevArgScan_Click(object sender, EventArgs e)
{
// Check if has reached the start
int index = argIndex - 1;
if (index == 0)
{
// If so disable the previous button
metroButtonPrevArgScan.Enabled = false;
}
AddNextArgSeries(index);
AddNextArgMS1Series(valKVP.Value[index]);
ValidationUIUtilities.FillCitIonGrid(metroGridArgIons, valKVP.Value[index]);
AddArgInfo(index);
metroButtonNextArgScan.Enabled = true;
ReturnArgIndex(index);
}
/// <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>
/// Go to the previous potential citrullination scan.
/// </summary>
private void MetroButtonPrevPotCitScan_Click(object sender, EventArgs e)
{
// Check if has reached the start
int index = potCitIndex - 1;
if (index == 0)
{
// If so, disable the previous button
metroButtonPrevPotCitScan.Enabled = false;
}
// Get the next potential citrullination series
AddNextPotCitSeries(index);
// Get the next potential citrullination series to MS1 chart
AddNextPotCitMS1Series(valKVP.Value[index]);
// Fill the ion grid
ValidationUIUtilities.FillArgIonGrid(metroGridPotCitIons, valKVP.Value[index], valKVP.Key);
// Enable the next button
metroButtonNextPotCitScan.Enabled = true;
// Add potential citrullination info to the window
AddPotCitInfo(index);
ReturnPotCitIndex(index);
}
/// <summary>
/// Create the image.
/// </summary>
/// <param name="directory">The directory the image should be saved to.</param>
/// <param name="result">The result the image should be created from.</param>
private void CreateImage(string directory, KeyValuePair <QuantResult, KeyValuePair <MsSpectrum, MsSpectrum> > result)
{
KeyValuePair <MsSpectrum, MsSpectrum> spectraData = result.Value;
// Get the filename
string baseFilename = string.Format("{0}_{1}_{2}", result.Key.Protein.Split('|')[0], result.Key.Sequence, result.Key.ValidationBy);
string filename = FileReader.GenerateFileName(directory, baseFilename, "tiff");
// Append the file to the annotation writer
if (_createAnnotationFile)
{
_annotationWriter.AppendLine($"** {filename.Split(new string[] { @"\" }, System.StringSplitOptions.None).Last() } **");
}
// From the validation type, create the graph
if (result.Key.ValidationBy == "Lone")
{
ValidationUIUtilities.CreateLoneCitMs2Chart(chartMS2, spectraData.Key);
ValidationUIUtilities.AnnotateSingleSpectra(chartMS2, spectraData.Key, HelperUtilities.CreateAAArray(result.Key.Sequence), true, _createAnnotationFile, _annotationWriter);
}
else
{
ValidationUIUtilities.CreatePairedMs2Chart(chartMS2, spectraData.Key, spectraData.Value);
ValidationUIUtilities.AnnotatePairedSpectra(chartMS2, spectraData.Key, spectraData.Value, HelperUtilities.CreateAAArray(result.Key.Sequence), _createAnnotationFile, _annotationWriter);
}
// Clear the old titles
chartMS2.Titles.Clear();
// And add a new one
chartMS2.Titles.Add(string.Format("{0}_{1}_{2}", result.Key.Protein.Split('|')[0], result.Key.Sequence, result.Key.ValidationBy));
chartMS2.Titles[0].Font = new Font(chartMS2.Titles[0].Font.FontFamily, 13F);
chartMS2.Titles[0].IsDockedInsideChartArea = false;
chartMS2.Titles[0].Docking = Docking.Top;
chartMS2.Titles[0].DockingOffset = 10;
chartMS2.SaveImage(filename, ChartImageFormat.Tiff);
ValidationUIUtilities.ClearChart(chartMS2);
chartMS2.Annotations.Clear();
}
/// <summary>
/// Go to the next arginine scan.
/// </summary>
private void MetroButtonNextArgScan_Click(object sender, EventArgs e)
{
// Check if has reached the end
int length = valKVP.Value.Count() - 1;
int index = argIndex + 1;
if (index == length)
{
// If so, disable the next button
metroButtonNextArgScan.Enabled = false;
}
// Get the next arginine series
AddNextArgSeries(index);
// Get the next arginine MS1 series
AddNextArgMS1Series(valKVP.Value[index]);
// Fill the ion grid
ValidationUIUtilities.FillCitIonGrid(metroGridArgIons, valKVP.Value[index]);
// Add arginine information
AddArgInfo(index);
// Disbale the previous button
metroButtonPrevArgScan.Enabled = true;
ReturnArgIndex(index);
}
/// <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>
/// Add the next potential citrullination series.
/// </summary>
/// <param name="index">The series index.</param>
private void AddNextPotCitSeries(int index)
{
ValidationUIUtilities.ClearChart(chartMS2);
ValidationUIUtilities.CreatePairedMs2Chart(chartMS2, valKVP.Value[index], valKVP.Key);
}