public static void ExportMsMs(this UMCClusterLight cluster, string path, List <DatasetInformation> datasets,
IMsMsSpectraWriter writer)
{
// Let's map the datasets first.
var readers = new Dictionary <int, ISpectraProvider>();
var information = new Dictionary <int, DatasetInformation>();
datasets.ForEach(x => information.Add(x.DatasetId, x));
// We are only loading what datasets we have to here!
// The point is, each cluster or feature may have come from a different raw data source...
// since we dont store all of the data in memory, we have to fetch it from the appropriate source.
// This means that we have to go into the raw data and get the scans for an MSMS spectra.
foreach (var feature in cluster.Features)
{
if (!readers.ContainsKey(feature.GroupId))
{
if (information.ContainsKey(feature.GroupId))
{
var singleInfo = information[feature.GroupId];
if (singleInfo.RawFile != null)
{
// Make sure that we have a file.
if (!File.Exists(singleInfo.RawFile.Path))
{
continue;
}
/// <summary>
/// Default constructor.
/// </summary>
/// <param name="path"></param>
public UMCClusterMsmsSpectraWriter(string name, IMsMsSpectraWriter spectraWriter, string extension)
: base(true)
{
m_spectraWriter = spectraWriter;
Extension = extension;
Name = name;
Description = "Writes the a cluster and the associated MS/MS meta-data.";
}
/// <summary>
/// Default constructor.
/// </summary>
/// <param name="path"></param>
public UMCClusterMsmsSpectraWriter(string name, IMsMsSpectraWriter spectraWriter, string extension)
: base(true)
{
m_spectraWriter = spectraWriter;
Extension = extension;
Name = name;
Description = "Writes the a cluster and the associated MS/MS meta-data.";
}
/// <summary>
/// Creates a spectra writer based on the file type.
/// </summary>
/// <param name="writerType"></param>
/// <returns></returns>
public static IMsMsSpectraWriter CreateSpectraWriter(string extension)
{
IMsMsSpectraWriter writer = null;
switch (extension)
{
case ".dta":
writer = CreateSpectraWriter(MsMsWriterType.DTA);
break;
case ".mgf":
writer = CreateSpectraWriter(MsMsWriterType.MGF);
break;
}
return(writer);
}
/// <summary>
/// Creates a spectra writer based on the file type.
/// </summary>
/// <param name="writerType"></param>
/// <returns></returns>
public static IMsMsSpectraWriter CreateSpectraWriter(MsMsWriterType writerType)
{
IMsMsSpectraWriter writer = null;
switch (writerType)
{
case MsMsWriterType.DTA:
writer = new DtaFileWriter();
break;
case MsMsWriterType.MGF:
writer = new MgfFileWriter();
break;
default:
break;
}
return(writer);
}
public static void ExportMsMs(this UMCClusterLight cluster, string path, List<DatasetInformation> datasets,
IMsMsSpectraWriter writer)
{
// Let's map the datasets first.
var readers = new Dictionary<int, ISpectraProvider>();
var information = new Dictionary<int, DatasetInformation>();
datasets.ForEach(x => information.Add(x.DatasetId, x));
// We are only loading what datasets we have to here!
// The point is, each cluster or feature may have come from a different raw data source...
// since we dont store all of the data in memory, we have to fetch it from the appropriate source.
// This means that we have to go into the raw data and get the scans for an MSMS spectra.
foreach (var feature in cluster.Features)
{
if (!readers.ContainsKey(feature.GroupId))
{
if (information.ContainsKey(feature.GroupId))
{
var singleInfo = information[feature.GroupId];
if (singleInfo.Raw != null && singleInfo.RawPath != null)
{
// Make sure that we have a file.
if (!File.Exists(singleInfo.RawPath))
continue;
// Here we create a data file reader for the file we want to access.
var provider = RawLoaderFactory.CreateFileReader(singleInfo.RawPath);
// Then we make sure we key it to the provider.
provider.AddDataFile(singleInfo.RawPath, feature.GroupId);
// Then make sure we map it for a dataset, so when we sort through a cluster
// we make sure that we can access in O(1) time.
readers.Add(feature.GroupId, provider);
}
}
}
}
// We flag the first write, so that if the file exists, we overwrite. They should have done
// checking to make sure that the file was already created...we dont care.
var firstWrite = true;
foreach (var feature in cluster.Features)
{
if (readers.ContainsKey(feature.GroupId))
{
var provider = readers[feature.GroupId];
foreach (var msFeature in feature.MsFeatures)
{
foreach (var spectrum in msFeature.MSnSpectra)
{
var summary = new ScanSummary();
var data = provider.GetRawSpectra(spectrum.Scan, spectrum.GroupId, out summary);
spectrum.Peaks = data;
spectrum.ScanMetaData = summary;
}
if (firstWrite)
{
writer.Write(path, msFeature.MSnSpectra);
}
else
{
writer.Append(path, msFeature.MSnSpectra);
}
}
}
}
}
