/// <summary>
/// Append a custom m/z value to CustomMZSearchValues
/// </summary>
/// <param name="mzSearchSpec"></param>
public void AddMzSearchTarget(clsCustomMZSearchSpec mzSearchSpec)
{
if (CustomMZSearchValues.Count > 0)
{
RawTextMZList += ",";
RawTextMZToleranceDaList += ",";
RawTextScanOrAcqTimeCenterList += ",";
RawTextScanOrAcqTimeToleranceList += ",";
}
RawTextMZList += mzSearchSpec.MZ.ToString(CultureInfo.InvariantCulture);
RawTextMZToleranceDaList += mzSearchSpec.MZToleranceDa.ToString(CultureInfo.InvariantCulture);
RawTextScanOrAcqTimeCenterList += mzSearchSpec.ScanOrAcqTimeCenter.ToString(CultureInfo.InvariantCulture);
RawTextScanOrAcqTimeToleranceList += mzSearchSpec.ScanOrAcqTimeTolerance.ToString(CultureInfo.InvariantCulture);
CustomMZSearchValues.Add(mzSearchSpec);
}
public bool SetCustomSICListValues(
eCustomSICScanTypeConstants eScanType,
double mzToleranceDa,
float scanOrAcqTimeToleranceValue,
double[] mzList,
double[] mzToleranceList,
float[] scanOrAcqTimeCenterList,
float[] scanOrAcqTimeToleranceList,
string[] scanComments)
{
if (mzToleranceList.Length > 0 && mzToleranceList.Length != mzList.Length)
{
// Invalid Custom SIC comment list; number of entries doesn't match
return(false);
}
if (scanOrAcqTimeCenterList.Length > 0 && scanOrAcqTimeCenterList.Length != mzList.Length)
{
// Invalid Custom SIC scan center list; number of entries doesn't match
return(false);
}
if (scanOrAcqTimeToleranceList.Length > 0 && scanOrAcqTimeToleranceList.Length != mzList.Length)
{
// Invalid Custom SIC scan center list; number of entries doesn't match
return(false);
}
if (scanComments.Length > 0 && scanComments.Length != mzList.Length)
{
// Invalid Custom SIC comment list; number of entries doesn't match
return(false);
}
ResetMzSearchValues();
ScanToleranceType = eScanType;
// This value is used if scanOrAcqTimeToleranceList is blank or for any entries in scanOrAcqTimeToleranceList() that are zero
ScanOrAcqTimeTolerance = scanOrAcqTimeToleranceValue;
if (mzList.Length == 0)
{
return(true);
}
for (var index = 0; index < mzList.Length; index++)
{
var mzSearchSpec = new clsCustomMZSearchSpec(mzList[index]);
if (mzToleranceList.Length > index && mzToleranceList[index] > 0)
{
mzSearchSpec.MZToleranceDa = mzToleranceList[index];
}
else
{
mzSearchSpec.MZToleranceDa = mzToleranceDa;
}
if (scanOrAcqTimeCenterList.Length > index)
{
mzSearchSpec.ScanOrAcqTimeCenter = scanOrAcqTimeCenterList[index];
}
else
{
mzSearchSpec.ScanOrAcqTimeCenter = 0;
} // Set to 0 to indicate that the entire file should be searched
if (scanOrAcqTimeToleranceList.Length > index && scanOrAcqTimeToleranceList[index] > 0)
{
mzSearchSpec.ScanOrAcqTimeTolerance = scanOrAcqTimeToleranceList[index];
}
else
{
mzSearchSpec.ScanOrAcqTimeTolerance = scanOrAcqTimeToleranceValue;
}
if (scanComments.Length > 0 && scanComments.Length > index)
{
mzSearchSpec.Comment = scanComments[index];
}
else
{
mzSearchSpec.Comment = string.Empty;
}
AddMzSearchTarget(mzSearchSpec);
}
ValidateCustomSICList();
return(true);
}
/// <summary>
/// Parse parallel lists of custom m/z info
/// </summary>
/// <param name="mzList">Comma or tab separated list of m/z values</param>
/// <param name="mzToleranceDaList">Comma or tab separated list of tolerances (in Da)</param>
/// <param name="scanCenterList">Comma or tab separated list of scan centers</param>
/// <param name="scanToleranceList">Comma or tab separated list of scan tolerances</param>
/// <param name="scanCommentList">Comma or tab separated list of comments</param>
/// <returns></returns>
public bool ParseCustomSICList(
string mzList,
string mzToleranceDaList,
string scanCenterList,
string scanToleranceList,
string scanCommentList)
{
var delimiters = new[] { ',', '\t' };
// Trim any trailing tab characters
mzList = mzList.TrimEnd('\t');
mzToleranceDaList = mzToleranceDaList.TrimEnd('\t');
scanCenterList = scanCenterList.TrimEnd('\t');
scanToleranceList = scanToleranceList.TrimEnd('\t');
scanCommentList = scanCommentList.TrimEnd(delimiters);
var mzValues = mzList.Split(delimiters).ToList();
var mzToleranceDa = mzToleranceDaList.Split(delimiters).ToList();
var scanCenters = scanCenterList.Split(delimiters).ToList();
var scanTolerances = scanToleranceList.Split(delimiters).ToList();
List <string> lstScanComments;
if (scanCommentList.Length > 0)
{
lstScanComments = scanCommentList.Split(delimiters).ToList();
}
else
{
lstScanComments = new List <string>();
}
ResetMzSearchValues();
if (mzValues.Count <= 0)
{
// Nothing to parse; return true
return(true);
}
for (var index = 0; index < mzValues.Count; index++)
{
if (!double.TryParse(mzValues[index], out var targetMz))
{
continue;
}
var mzSearchSpec = new clsCustomMZSearchSpec(targetMz)
{
MZToleranceDa = 0,
ScanOrAcqTimeCenter = 0, // Set to 0 to indicate that the entire file should be searched
ScanOrAcqTimeTolerance = 0
};
if (scanCenters.Count > index)
{
if (clsUtilities.IsNumber(scanCenters[index]))
{
if (ScanToleranceType == eCustomSICScanTypeConstants.Absolute)
{
mzSearchSpec.ScanOrAcqTimeCenter = int.Parse(scanCenters[index]);
}
else
{
// Includes .Relative and .AcquisitionTime
mzSearchSpec.ScanOrAcqTimeCenter = float.Parse(scanCenters[index]);
}
}
}
if (scanTolerances.Count > index)
{
if (clsUtilities.IsNumber(scanTolerances[index]))
{
if (ScanToleranceType == eCustomSICScanTypeConstants.Absolute)
{
mzSearchSpec.ScanOrAcqTimeTolerance = int.Parse(scanTolerances[index]);
}
else
{
// Includes .Relative and .AcquisitionTime
mzSearchSpec.ScanOrAcqTimeTolerance = float.Parse(scanTolerances[index]);
}
}
}
if (mzToleranceDa.Count > index)
{
if (clsUtilities.IsNumber(mzToleranceDa[index]))
{
mzSearchSpec.MZToleranceDa = double.Parse(mzToleranceDa[index]);
}
}
if (lstScanComments.Count > index)
{
mzSearchSpec.Comment = lstScanComments[index];
}
else
{
mzSearchSpec.Comment = string.Empty;
}
AddMzSearchTarget(mzSearchSpec);
}
return(true);
}
