/// <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); } } } }