/// <summary>
/// Updates the program's settings using the .ini settings file passed to the constructor
/// </summary>
public void UpdateSettings()
{
/*
* Files Settings
*/
var inputFilePath = GetValueForKey("Files", "InputFileName");
if (!string.IsNullOrWhiteSpace(inputFilePath))
{
var directoryName = Path.GetDirectoryName(inputFilePath);
if (directoryName != null && !directoryName.Equals(string.Empty))
{
Settings.InputDirectory = Path.GetDirectoryName(inputFilePath) + "\\";
}
Settings.InputFileName = Path.GetFileName(inputFilePath);
}
var outputDirectory = GetValueForKey("Files", "OutputDirectory");
if (!string.IsNullOrWhiteSpace(outputDirectory))
{
Settings.OutputDirectory = outputDirectory + "\\";
}
else
{
Settings.OutputDirectory = Settings.InputDirectory;
}
var deconToolsFilterFile = GetValueForKey("Files", "DeconToolsFilterFileName");
if (!string.IsNullOrWhiteSpace(deconToolsFilterFile))
{
Settings.DeconToolsFilterFileName = deconToolsFilterFile;
Console.WriteLine("Reading " + deconToolsFilterFile);
var loader = new DeconToolsFilterLoader(deconToolsFilterFile);
loader.DisplayFilters();
Settings.DeconToolsFilterList = loader.DeconToolsFilterList;
}
else
{
Settings.DeconToolsFilterList = new List <DeconToolsFilter>();
}
/*
* DataFilters Settings
*/
var maxIsotopicFit = GetValueForKey("DataFilters", "MaxIsotopicFit");
if (!string.IsNullOrWhiteSpace(maxIsotopicFit))
{
Settings.FitMax = float.Parse(maxIsotopicFit);
}
var maxIScore = GetValueForKey("DataFilters", "MaxIScore");
if (!string.IsNullOrWhiteSpace(maxIScore))
{
Settings.InterferenceScoreMax = float.Parse(maxIScore);
}
var minimumIntensity = GetValueForKey("DataFilters", "MinimumIntensity");
if (!string.IsNullOrWhiteSpace(minimumIntensity))
{
Settings.IntensityMin = float.Parse(minimumIntensity);
}
var useHardCodedFilters = GetValueForKey("DataFilters", "UseHardCodedFilters");
if (!string.IsNullOrWhiteSpace(useHardCodedFilters))
{
Settings.FilterUsingHardCodedFilters = bool.Parse(useHardCodedFilters);
}
var filterFlaggedData = GetValueForKey("DataFilters", "FilterFlaggedData");
if (!string.IsNullOrWhiteSpace(filterFlaggedData))
{
Settings.FilterFlaggedData = bool.Parse(filterFlaggedData);
}
var imsMinScan = GetValueForKey("DataFilters", "IMSMinScan");
if (!string.IsNullOrWhiteSpace(imsMinScan))
{
Settings.ScanIMSMin = int.Parse(imsMinScan);
}
var imsMaxScan = GetValueForKey("DataFilters", "IMSMaxScan");
if (!string.IsNullOrWhiteSpace(imsMaxScan))
{
Settings.ScanIMSMax = int.Parse(imsMaxScan);
if (Settings.ScanIMSMax <= 0)
{
Settings.ScanIMSMax = int.MaxValue;
}
}
var lcMinScan = GetValueForKey("DataFilters", "LCMinScan");
if (!string.IsNullOrWhiteSpace(lcMinScan))
{
Settings.ScanLCMin = int.Parse(lcMinScan);
}
var lcMaxScan = GetValueForKey("DataFilters", "LCMaxScan");
if (!string.IsNullOrWhiteSpace(lcMaxScan))
{
Settings.ScanLCMax = int.Parse(lcMaxScan);
if (Settings.ScanLCMax <= 0)
{
Settings.ScanLCMax = int.MaxValue;
}
}
var monoisotopicMassMin = GetValueForKey("DataFilters", "MonoMassStart");
if (!string.IsNullOrWhiteSpace(monoisotopicMassMin))
{
Settings.MassMonoisotopicStart = float.Parse(monoisotopicMassMin);
}
var monoisotopicMassMax = GetValueForKey("DataFilters", "MonoMassEnd");
if (!string.IsNullOrWhiteSpace(monoisotopicMassMax))
{
Settings.MassMonoisotopicEnd = float.Parse(monoisotopicMassMax);
}
var frameTypeFilter = GetValueForKey("DataFilters", "FrameType");
if (!string.IsNullOrWhiteSpace(frameTypeFilter))
{
Settings.FrameTypeFilter = (UIMFData.FrameType) short.Parse(frameTypeFilter);
}
/*
* UMCCreationOptions Settings
*/
var ignoreImsDriftTime = GetValueForKey("UMCCreationOptions", "IgnoreIMSDriftTime");
if (!string.IsNullOrWhiteSpace(ignoreImsDriftTime))
{
Settings.IgnoreIMSDriftTime = bool.Parse(ignoreImsDriftTime);
}
// Monoisotopic mass constraint, in ppm
var monoMassConstraint = GetValueForKey("UMCCreationOptions", "MonoMassConstraint");
if (!string.IsNullOrWhiteSpace(monoMassConstraint))
{
Settings.MassMonoisotopicConstraint = float.Parse(monoMassConstraint);
}
// Obsolete:
// var monoMassConstraintIsPPM = GetValueForKey("UMCCreationOptions", "MonoMassConstraintIsPPM");
// Obsolete:
// var useGenericNET = GetValueForKey("UMCCreationOptions", "UseGenericNET");
var useCharge = GetValueForKey("UMCCreationOptions", "UseCharge");
if (!string.IsNullOrWhiteSpace(useCharge))
{
Settings.UseCharge = bool.Parse(useCharge);
}
var minFeatureLengthPoints = GetValueForKey("UMCCreationOptions", "MinFeatureLengthPoints");
if (!string.IsNullOrWhiteSpace(minFeatureLengthPoints))
{
Settings.FeatureLengthMin = short.Parse(minFeatureLengthPoints);
}
var lcGapMaxSize = GetValueForKey("UMCCreationOptions", "LCGapMaxSize");
if (!string.IsNullOrWhiteSpace(lcGapMaxSize))
{
Settings.LCGapSizeMax = short.Parse(lcGapMaxSize);
}
var imsMaxDaCorrection = GetValueForKey("UMCCreationOptions", "IMSMaxDaCorrection");
if (!string.IsNullOrWhiteSpace(imsMaxDaCorrection))
{
int readValue = short.Parse(imsMaxDaCorrection);
Settings.IMSDaCorrectionMax = readValue < 0 ? 0 : readValue;
}
// Obsolete:
// var umcFitScoreMinimum = GetValueForKey("UMCCreationOptions", "UMCFitScoreMinimum");
// Obsolete: splitting is always enabled when finding LC-IMS-MS features
// umcSplittingEnabled = GetValueForKey("UMCSplittingOptions", "Split");
// Obsolete (not implemented)
// minimumDifferenceInMedianPpmMass = GetValueForKey("UMCSplittingOptions", "MinimumDifferenceInMedianPpmMassToSplit");
/*
* DriftProfile Settings
*/
var useConformationDetection = GetValueForKey("DriftProfileOptions", "UseConformationDetection");
if (!string.IsNullOrWhiteSpace(useConformationDetection))
{
Settings.UseConformationDetection = bool.Parse(useConformationDetection);
}
var smoothingStDev = GetValueForKey("DriftProfileOptions", "SmoothingStDev");
if (!string.IsNullOrWhiteSpace(smoothingStDev))
{
Settings.SmoothingStDev = float.Parse(smoothingStDev);
}
/*
* PostCreationFiltering Settings
*/
var filterIsosToSinglePoint = GetValueForKey("PostCreationFilteringOptions", "FilterIsosToSinglePoint");
if (!string.IsNullOrWhiteSpace(filterIsosToSinglePoint))
{
Settings.FilterIsosToSinglePoint = bool.Parse(filterIsosToSinglePoint);
}
}
public void CreateSettings()
{
/*
* Files Settings
*/
var value = IniReadValue("Files", "InputFileName");
if (!string.IsNullOrWhiteSpace(value))
{
var directoryName = Path.GetDirectoryName(value);
if (directoryName != null && !directoryName.Equals(string.Empty))
{
Settings.InputDirectory = Path.GetDirectoryName(value) + "\\";
}
Settings.InputFileName = Path.GetFileName(value);
}
value = IniReadValue("Files", "OutputDirectory");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.OutputDirectory = value + "\\";
}
else
{
Settings.OutputDirectory = Settings.InputDirectory;
}
value = IniReadValue("Files", "DeconToolsFilterFileName");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.DeconToolsFilterFileName = value;
var loader = new DeconToolsFilterLoader(value);
Settings.DeconToolsFilterList = loader.DeconToolsFilterList;
}
else
{
Settings.DeconToolsFilterList = new System.Collections.Generic.List <DeconToolsFilter>();
}
/*
* DataFilters Settings
*/
value = IniReadValue("DataFilters", "MaxIsotopicFit");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.FitMax = float.Parse(value);
}
value = IniReadValue("DataFilters", "MaxIScore");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.InterferenceScoreMax = float.Parse(value);
}
value = IniReadValue("DataFilters", "MinimumIntensity");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.IntensityMin = float.Parse(value);
}
value = IniReadValue("DataFilters", "UseHardCodedFilters");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.FilterUsingHardCodedFilters = bool.Parse(value);
}
value = IniReadValue("DataFilters", "FilterFlaggedData");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.FilterFlaggedData = bool.Parse(value);
}
value = IniReadValue("DataFilters", "IMSMinScan");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.ScanIMSMin = int.Parse(value);
}
value = IniReadValue("DataFilters", "IMSMaxScan");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.ScanIMSMax = int.Parse(value);
if (Settings.ScanIMSMax <= 0)
{
Settings.ScanIMSMax = int.MaxValue;
}
}
value = IniReadValue("DataFilters", "LCMinScan");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.ScanLCMin = int.Parse(value);
}
value = IniReadValue("DataFilters", "LCMaxScan");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.ScanLCMax = int.Parse(value);
if (Settings.ScanLCMax <= 0)
{
Settings.ScanLCMax = int.MaxValue;
}
}
value = IniReadValue("DataFilters", "MonoMassStart");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.MassMonoisotopicStart = float.Parse(value);
}
value = IniReadValue("DataFilters", "MonoMassEnd");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.MassMonoisotopicEnd = float.Parse(value);
}
value = IniReadValue("DataFilters", "FrameType");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.FrameTypeFilter = (DataReader.FrameType) short.Parse(value);
}
/*
* UMCCreationOptions Settings
*/
value = IniReadValue("UMCCreationOptions", "IgnoreIMSDriftTime");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.IgnoreIMSDriftTime = bool.Parse(value);
}
value = IniReadValue("UMCCreationOptions", "MonoMassConstraint");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.MassMonoisotopicConstraint = float.Parse(value);
}
value = IniReadValue("UMCCreationOptions", "MonoMassConstraintIsPPM");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.MassMonoisotopicConstraintIsPPM = bool.Parse(value);
}
value = IniReadValue("UMCCreationOptions", "UseGenericNET");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.UseGenericNET = bool.Parse(value);
}
value = IniReadValue("UMCCreationOptions", "UseCharge");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.UseCharge = bool.Parse(value);
}
value = IniReadValue("UMCCreationOptions", "MinFeatureLengthPoints");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.FeatureLengthMin = short.Parse(value);
}
value = IniReadValue("UMCCreationOptions", "LCGapMaxSize");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.LCGapSizeMax = short.Parse(value);
}
value = IniReadValue("UMCCreationOptions", "IMSMaxDaCorrection");
if (!string.IsNullOrWhiteSpace(value))
{
int readValue = short.Parse(value);
Settings.IMSDaCorrectionMax = readValue < 0 ? 0 : readValue;
}
value = IniReadValue("UMCCreationOptions", "UMCFitScoreMinimum");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.UMCFitScoreMinimum = float.Parse(value);
}
/*
* UMCSplittingOptions Settings
*/
value = IniReadValue("UMCSplittingOptions", "Split");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.Split = bool.Parse(value);
}
value = IniReadValue("UMCSplittingOptions", "MinimumDifferenceInMedianPpmMassToSplit");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.MinimumDifferenceInMedianPpmMassToSplit = short.Parse(value);
}
/*
* DriftProfile Settings
*/
value = IniReadValue("DriftProfileOptions", "UseConformationDetection");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.UseConformationDetection = bool.Parse(value);
}
value = IniReadValue("DriftProfileOptions", "SmoothingStDev");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.SmoothingStDev = float.Parse(value);
}
/*
* PostCreationFiltering Settings
*/
value = IniReadValue("PostCreationFilteringOptions", "FilterIsosToSinglePoint");
if (!string.IsNullOrWhiteSpace(value))
{
Settings.FilterIsosToSinglePoint = bool.Parse(value);
}
}
