public NetAlignmentInfo DoNetAlignment(bool recollectResultsIfAlreadyPresent = false)
{
var needToProcessResults = (recollectResultsIfAlreadyPresent ||
(IqResultsForAlignment == null || IqResultsForAlignment.Count == 0));
if (needToProcessResults)
{
Execute(Targets);
IqResultsForAlignment = FilterAlignmentResults();
}
IqResultsForNetAlignment = UpdateMsgfTargetsWithDatabaseNetValues(IqResultsForAlignment);
IqLogger.Log.Info("Applying Loess smoothing to NET alignment data. LoessBandwidth= " + LoessBandwidthNetAlignment);
var netAlignmentDataForLoess = PrepareNetAlignmentDataForLoessSmoothing();
var iterationsForNetAlignment = 2;
var loessInterpolatorForNetAlignment = new LoessInterpolator(LoessBandwidthNetAlignment, iterationsForNetAlignment);
var loessSmoothedData = new XYData();
loessSmoothedData.Xvalues = netAlignmentDataForLoess.Select(p => p.Scan).ToArray();
loessSmoothedData.Yvalues = loessInterpolatorForNetAlignment.Smooth(netAlignmentDataForLoess.Select(p => p.Scan).ToArray(),
netAlignmentDataForLoess.Select(p => p.NET).ToArray());
var scanToNetVals = new List <ScanNETPair>();
for (var i = 0; i < loessSmoothedData.Xvalues.Length; i++)
{
var xval = loessSmoothedData.Xvalues[i];
var yval = loessSmoothedData.Yvalues[i];
if (!double.IsNaN(yval))
{
var scanNETPair = new ScanNETPair(xval, yval);
scanToNetVals.Add(scanNETPair);
}
}
var netAlignmentInfo = new NetAlignmentInfoBasic(Run.MinLCScan, Run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scanToNetVals);
IqLogger.Log.Info("NET alignment complete using " + scanToNetVals.Count + " data points.");
NetAlignmentInfo = netAlignmentInfo;
return(netAlignmentInfo);
}
public static bool AlignRunUsingAlignmentInfoInFiles(Run run, string alignmentDataFolder = "")
{
bool alignmentSuccessful;
string basePath;
if (string.IsNullOrEmpty(alignmentDataFolder))
{
basePath = run.DataSetPath;
}
else
{
if (Directory.Exists(alignmentDataFolder))
{
basePath = alignmentDataFolder;
}
else
{
throw new DirectoryNotFoundException(
"Cannot align dataset. Source alignment folder does not exist. Alignment folder = " +
alignmentDataFolder);
}
}
var expectedMZAlignmentFile = Path.Combine(basePath, run.DatasetName + "_MZAlignment.txt");
var expectedNETAlignmentFile = Path.Combine(basePath, run.DatasetName + "_NETAlignment.txt");
//first will try to load the multiAlign alignment info
if (File.Exists(expectedMZAlignmentFile))
{
var importer = new MassAlignmentInfoFromTextImporter(expectedMZAlignmentFile);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
}
if (File.Exists(expectedNETAlignmentFile))
{
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(expectedNETAlignmentFile);
var scanNETList = netAlignmentInfoImporter.Import();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scanNETList);
run.NetAlignmentInfo = netAlignmentInfo;
}
//if still not aligned, try to get the NET alignment from UMCs file. (this is the older way to do it)
if (run.NETIsAligned)
{
alignmentSuccessful = true;
}
else
{
var alignmentDirInfo = new DirectoryInfo(basePath);
var umcFileInfo = alignmentDirInfo.GetFiles("*_umcs.txt");
var umcFileCount = umcFileInfo.Count();
if (umcFileCount == 1)
{
var targetUmcFileName = umcFileInfo.First().FullName;
var importer = new UMCFileImporter(targetUmcFileName, '\t');
var umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
run.NetAlignmentInfo = netAlignmentInfo;
Console.WriteLine(run.DatasetName + " aligned.");
alignmentSuccessful = true;
}
else if (umcFileCount > 1)
{
var expectedUMCName = Path.Combine(basePath, run.DatasetName + "_UMCs.txt");
if (File.Exists(expectedUMCName))
{
var importer = new UMCFileImporter(expectedUMCName, '\t');
var umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
run.NetAlignmentInfo = netAlignmentInfo;
Console.WriteLine(run.DatasetName + " NET aligned using UMC file: " + expectedUMCName);
alignmentSuccessful = true;
}
else
{
throw new FileNotFoundException("Trying to align dataset: " + run.DatasetName +
" but UMC file not found.");
}
}
else
{
Console.WriteLine(run.DatasetName + " is NOT NET aligned.");
alignmentSuccessful = false;
}
}
//mass is still not aligned... use data in viper output file: _MassAndGANETErrors_BeforeRefinement.txt
if (run.MassIsAligned == false)
{
var expectedViperMassAlignmentFile = Path.Combine(basePath, run.DatasetName + "_MassAndGANETErrors_BeforeRefinement.txt");
if (File.Exists(expectedViperMassAlignmentFile))
{
var importer = new ViperMassCalibrationLoader(expectedViperMassAlignmentFile);
var viperCalibrationData = importer.ImportMassCalibrationData();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(viperCalibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
Console.WriteLine(run.DatasetName + "- mass aligned using file: " + expectedViperMassAlignmentFile);
alignmentSuccessful = true;
}
else
{
Console.WriteLine(run.DatasetName + " is NOT mass aligned");
}
}
return(alignmentSuccessful);
}
