public IFileReader2 <List <SrmTransition> > GetReader()
{
var result = SrmFormatFactory.FindReader(this.DefinitionFileFormat);
if (result == null)
{
result = SrmFormatFactory.GetDefaultReader();
}
return(result);
}
private void btnSave_Click(object sender, EventArgs e)
{
for (int i = 0; i < items.Count; i++)
{
if (!string.IsNullOrEmpty(items[i].PropertyName))
{
if (!propertyNames.Contains(items[i].PropertyName))
{
MessageBox.Show("Property " + items[i].PropertyName + " is illegal!");
return;
}
for (int j = i + 1; j < items.Count; j++)
{
if (items[i].PropertyName.Equals(items[j].PropertyName))
{
MessageBox.Show("Property " + items[i].PropertyName + " are multi-defined!");
return;
}
}
}
}
dlgSaveFormatFile.InitialDirectory = FileUtils.GetTemplateDir().FullName;
if (File.Exists(lastFile) && !File.Exists(dlgSaveFormatFile.FileName))
{
dlgSaveFormatFile.FileName = lastFile;
}
if (dlgSaveFormatFile.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
var map = headers.ToDictionary(m => m.PropertyName);
items.ForEach(m =>
{
if (!string.IsNullOrEmpty(m.PropertyName))
{
var item = map[m.PropertyName];
m.ValueType = item.ValueType;
m.Required = item.Required;
m.Format = item.Format;
}
});
items.DelimiterString = txtDelimiter.Text;
items.Description = txtDescription.Text;
items.WriteToFile(dlgSaveFormatFile.FileName);
SrmFormatFactory.Refresh();
}
}
public SrmDistillerUI()
{
InitializeComponent();
base.SetDirectoryArgument("TargetDirectory", "Target");
this.dataDirs = new RcpaListViewMultipleFileDirectoryField(
this.btnAddFiles,
this.btnAddDirectory,
this.btnAddSubdirectory,
this.btnRemove,
this.btnLoad,
this.btnSave,
this.lvDirectories,
"Files",
new OpenFileArgument("mzXml / mzData / Thermo Raw", new string[] { "mzXml", "mzData", "raw" }),
"Agilent .d directory",
true,
true);
AddComponent(this.dataDirs);
this.rtToleranceInSecond = new RcpaDoubleField(txtRetentionTimeTolerance, "RTToleranceSecond", "Retention Time Tolerance in Second", 1.0, true);
AddComponent(this.rtToleranceInSecond);
this.signalToNoise = new RcpaDoubleField(txtSignalToNoise, "SignalToNoise", "Signal to Noise", 3.0, true);
AddComponent(this.signalToNoise);
this.precursorMassDistance = new RcpaTextField(txtPrecursorTolerance, "PrecursorMassDistance", "Distance between light and heavy precursor mass", "7,8,10", true);
AddComponent(this.precursorMassDistance);
this.smooth = new RcpaCheckBox(cbSmooth, "Smooth", true);
AddComponent(this.smooth);
this.refinePeakPicking = new RcpaCheckBox(cbRefinePeakPicking, "RefinePeakPicking", true);
AddComponent(this.refinePeakPicking);
this.deductBaseLine = new RcpaCheckBox(cbBaseLineExtraction, "DeductBaseLine", false);
AddComponent(this.deductBaseLine);
this.mzTolerance = new RcpaDoubleField(txtMzTolerance, "MzTolerance", "Product ion m/z tolerance", 0.1, true);
AddComponent(this.mzTolerance);
this.validateSignalToNoise = new RcpaDoubleField(txtValidateSignalToNoise, "ValidateSignalToNoise", "Validation signal to noise", 2, true);
AddComponent(this.validateSignalToNoise);
this.validateCorrel = new RcpaDoubleField(txtValidateCorrel, "ValidateCorrel", "Validation regression correlation", 0.5, true);
AddComponent(this.validateCorrel);
this.minValidTransactionPair = new RcpaIntegerField(txtMinValidTransactionPair, "minValidTransactionPair", "Minimum valid transaction pair count", 2, true);
AddComponent(this.minValidTransactionPair);
this.clusterByPredefine = new RcpaRadioButton(rbClusterByPredefine, "ClusterByPredefined", true);
AddComponent(this.clusterByPredefine);
this.clusterByRealData = new RcpaRadioButton(rbClusterByRealData, "ClusterByRealData", false);
AddComponent(this.clusterByRealData);
this.predefinedFile = new RcpaFileField(btnPredefined, txtPredefinedFile, "PredefinedFile", new OpenFileArgument("Predefined SRM Transaction File", ".txt"), false);
AddComponent(this.predefinedFile);
this.peakPickingByBaseline = new RcpaRadioButton(rbBaseline, "PeakPickingByBaseline", true);
AddComponent(this.peakPickingByBaseline);
this.peakPickingByHighestPeak = new RcpaRadioButton(rbHighestPeak, "PeakPickingByHighestPeak", false);
AddComponent(this.peakPickingByHighestPeak);
this.baseLinePercentage = new RcpaDoubleField(txtBaselinePercentage, "BaselinePercentage", "Baseline percentage", 5, true);
AddComponent(this.baseLinePercentage);
this.highestPeakPercentage = new RcpaDoubleField(txtHighestPeakPercentage, "HighestPeakPercentage", "Highest peak percentage", 5, false);
AddComponent(this.highestPeakPercentage);
this.precursorDistance = new RcpaDoubleField(txtMaxPrecursorDistance, "precursorDistance", "Maximum Precursor Distance", 20, true);
AddComponent(this.precursorDistance);
this.formats = new RcpaComboBox <IFileReader2 <List <SrmTransition> > >(cbFormat, "FileFormat", SrmFormatFactory.GetReaders().ToArray(), 0);
AddComponent(this.formats);
this.minEnabledScan = new RcpaIntegerField(txtMinEnabledScan, "MinValidScan", "Minimum valid scan count", 5, true);
AddComponent(this.minEnabledScan);
this.hasDecoy = new RcpaCheckBox(cbDecoyPattern, "HasDecoy", false);
AddComponent(this.hasDecoy);
this.ratioByArea = new RcpaCheckBox(cbRatioByArea, "ratioByArea", true);
AddComponent(this.ratioByArea);
this.decoyPattern = new RcpaTextField(txtDecoyPattern, "DecoyPattern", "Decoy pattern", "DECOY", false);
this.decoyPattern.ValidateFunc = m =>
{
try
{
new Regex(m);
return(true);
}
catch (Exception)
{
return(false);
}
};
AddComponent(this.decoyPattern);
this.Text = Constants.GetSQHTitle(title, version);
}