/// <summary>
/// Constructor, using an explicit threshold
/// </summary>
/// <param name="setThreshold"></param>
public MzIdentMLReader(double setThreshold)
{
IdentProg = IdentProgramType.Unset;
// Disable threshold stepping by setting currentSteps beyond maxSteps
_currentSteps = _maxSteps + 1;
_specEValueThreshold = setThreshold;
_mvhThreshold = setThreshold;
HaveScanTimes = false;
}
/// <summary>
/// Read the MZIdentML file and cache the data
/// </summary>
/// <param name="path">Path to *.mzid/mzIdentML file</param>
/// <returns>List of ScanData</returns>
public List <IdentData> Read(string path)
{
var psmResults = new List <IdentData>();
// Read in the file
var mzIdentMLData = new SimpleMZIdentMLReader().Read(path);
HaveScanTimes = false;
IdentProg = mzIdentMLData.AnalysisSoftware switch
{
"MyriMatch" => IdentProgramType.MyriMatch,
"MS-GF+" => IdentProgramType.MSGFPlus,
_ => IdentProgramType.Unset
};
while (true)
{
psmResults.Clear();
// Filter and process the data
foreach (var result in mzIdentMLData.Identifications)
{
ProcessSpectrumIdentificationResult(result, psmResults);
}
if (psmResults.Count >= 500)
{
OnStatusEvent(" {0:N0} PSMs passed the filters", psmResults.Count);
break;
}
OnStatusEvent(" Fewer than 500 PSMs passed the filters ({0})", psmResults.Count);
// Loosen the filters and try again (up to 3 times)
if (!AdjustThreshold())
{
if (psmResults.Count == 0)
{
OnWarningEvent(" No PSMs passed the filters");
}
else
{
OnStatusEvent(" Plotting errors using these PSMs");
}
break;
}
OnStatusEvent(" Loosening thresholds and trying again");
}
return(psmResults);
}
// ReSharper disable once UnusedMember.Global
/// <summary>
/// Constructor, using default thresholds
/// </summary>
public MzIdentMLReader()
{
IdentProg = IdentProgramType.Unset;
_currentSteps = 0;
}
