/// <summary>
/// Writes the opening tags and metadata information.
/// </summary>
/// <param name="header"></param>
public void WriteHeader(ScanFileHeader header)
{
writer.WriteStartElement("mzXML", "http://sashimi.sourceforge.net/schema_revision/mzXML_3.1");
writer.WriteAttributeString("xmlns", "xsi", null, "http://www.w3.org/2001/XMLSchema-instance");
writer.WriteAttributeString("xsi", "schemaLocation", null, "http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd");
writer.WriteStartElement("msRun");
writer.WriteAttributeString("scanCount", header.ScanCount.ToString());
writer.WriteAttributeString("startTime", MakeRetentionTimeString(header.StartTime));
writer.WriteAttributeString("endTime", MakeRetentionTimeString(header.EndTime));
writer.WriteStartElement("parentFile");
writer.WriteAttributeString("fileName", header.FileName);
writer.WriteAttributeString("fileType", "RAWData");
writer.WriteEndElement(); // parentFile
writer.WriteStartElement("msInstrument");
writer.WriteStartElement("msManufacturer");
writer.WriteAttributeString("category", "msManufacturer");
writer.WriteAttributeString("value", header.InstrumentManufacturer);
writer.WriteEndElement(); // msManufacturer
writer.WriteStartElement("msModel");
writer.WriteAttributeString("category", "msModel");
writer.WriteAttributeString("value", header.InstrumentModel);
writer.WriteEndElement(); // msModel
writer.WriteEndElement(); // msInstrument
}
/// <summary>
/// Writes the opening tags and metadata information.
/// </summary>
/// <param name="header"></param>
public void WriteHeader(ScanFileHeader header)
{
writer.WriteStartElement("mzXML", "http://sashimi.sourceforge.net/schema_revision/mzXML_3.1");
writer.WriteAttributeString("xmlns", "xsi", null, "http://www.w3.org/2001/XMLSchema-instance");
writer.WriteAttributeString("xsi", "schemaLocation", null, "http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd");
writer.WriteStartElement("msRun");
writer.WriteAttributeString("scanCount", header.ScanCount.ToString());
writer.WriteAttributeString("startTime", MakeRetentionTimeString(header.StartTime));
writer.WriteAttributeString("endTime", MakeRetentionTimeString(header.EndTime));
writer.WriteStartElement("parentFile");
writer.WriteAttributeString("fileName", header.FileName);
writer.WriteAttributeString("fileType", "RAWData");
writer.WriteAttributeString("fileSha1", CalculateFileHash(header.FilePath));
writer.WriteEndElement(); // parentFile
writer.WriteStartElement("dataProcessing");
writer.WriteStartElement("software");
writer.WriteAttributeString("type", "conversion");
writer.WriteAttributeString("name", "Monocle");
writer.WriteAttributeString("version", "1");
writer.WriteEndElement(); // software
writer.WriteEndElement(); // dataProcessing
}
public ScanFileHeader GetHeader()
{
var header = new ScanFileHeader();
header.StartTime = (float)rawFile.RunHeaderEx.StartTime;
header.EndTime = (float)rawFile.RunHeaderEx.EndTime;
header.ScanCount = rawFile.RunHeaderEx.SpectraCount;
header.InstrumentModel = rawFile.GetInstrumentData().Model;
header.InstrumentManufacturer = "ThermoFisher";
return(header);
}
/// <summary>
/// Writes the header for the file.
/// For mzdb, no information from the header is saved.
/// </summary>
public void WriteHeader(ScanFileHeader header)
{
string sql = "INSERT INTO metadata (name, value) VALUES ($name, $value)";
var command = new SQLiteCommand(sql, db);
command.Parameters.AddWithValue("$name", "version");
command.Parameters.AddWithValue("$value", "1");
command.ExecuteNonQuery();
command.Parameters.AddWithValue("$name", "compression");
command.Parameters.AddWithValue("$value", "none");
command.ExecuteNonQuery();
}
public void testOutput()
{
var reader = new MzXmlReader();
reader.Open("data/orbixl-mini.mzxml", new ScanReaderOptions());
string dir = Directory.GetCurrentDirectory();
var writer = new MzXmlWriter();
writer.Open("data/mzxml-writer-test.mzxml");
var header = new ScanFileHeader();
header.FileName = "mzxml-writer-test.mzxml";
header.FilePath = "data/mzxml-writer-test.mzxml";
writer.WriteHeader(header);
var scans = reader.GetEnumerator();
scans.MoveNext();
Scan scan1 = (Scan)scans.Current;
scans.MoveNext();
Scan scan2 = (Scan)scans.Current;
writer.WriteScan(scan1);
writer.WriteScan(scan2);
writer.Close();
reader = new MzXmlReader();
reader.Open("data/mzxml-writer-test.mzxml", new ScanReaderOptions());
scans = reader.GetEnumerator();
scans.MoveNext();
Scan scan3 = (Scan)scans.Current;
scans.MoveNext();
Scan scan4 = (Scan)scans.Current;
Assert.Equal(scan1.ScanNumber, scan3.ScanNumber);
Assert.Equal(scan1.RetentionTime, scan3.RetentionTime);
Assert.Equal(scan1.PeakCount, scan3.PeakCount);
Assert.Equal(scan1.Centroids[0].Mz, scan3.Centroids[0].Mz);
Assert.Equal(scan1.Centroids[11].Intensity, scan3.Centroids[11].Intensity);
}
public void WriteHeader(ScanFileHeader header)
{
writer.WriteStartDocument();
writer.WriteStartElement("indexedmzML", "http://psi.hupo.org/ms/mzml");
writer.WriteAttributeString("xmlns", "xsi", null, "http://www.w3.org/2001/XMLSchema-instance");
writer.WriteAttributeString("xsi", "schemaLocation", null, "http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd");
writer.WriteStartElement("mzML", "http://psi.hupo.org/ms/mzml");
writer.WriteAttributeString("xmlns", "xsi", null, "http://www.w3.org/2001/XMLSchema-instance");
writer.WriteAttributeString("xsi", "schemaLocation", null, "http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd");
writer.WriteAttributeString("version", "1.1.0");
writer.WriteAttributeString("id", Path.GetFileNameWithoutExtension(header.FileName));
writer.WriteStartElement("cvList");
writer.WriteAttributeString("count", "2");
writer.WriteStartElement("cv");
writer.WriteAttributeString("id", "MS");
writer.WriteAttributeString("fullName", "Proteomics Standards Initiative Mass Spectrometry Ontology");
writer.WriteAttributeString("version", "1.18.2");
writer.WriteAttributeString("URI", "http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo");
writer.WriteEndElement();
writer.WriteStartElement("cv");
writer.WriteAttributeString("id", "UO");
writer.WriteAttributeString("fullName", "Unit Ontology");
writer.WriteAttributeString("version", "04:03:2009");
writer.WriteAttributeString("URI", "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo");
writer.WriteEndElement();
writer.WriteEndElement();// cvlist
writer.WriteStartElement("fileDescription");
writer.WriteStartElement("fileContent");
WriteCVParam("MS:1000579", "");
WriteCVParam("MS:1000580", "");
writer.WriteEndElement(); // fileContent
writer.WriteEndElement(); // fileDescription
writer.WriteStartElement("softwareList");
writer.WriteAttributeString("count", "1");
writer.WriteStartElement("software");
writer.WriteAttributeString("id", "Monocle");
writer.WriteAttributeString("version", "1");
WriteCVParam("MS:1000799", "custom unreleased software tool");
writer.WriteEndElement(); // software
writer.WriteEndElement(); // softwareList
writer.WriteStartElement("instrumentConfigurationList");
writer.WriteAttributeString("count", "1");
writer.WriteStartElement("instrumentConfiguration");
writer.WriteAttributeString("id", "IC1");
writer.WriteStartElement("softwareRef");
writer.WriteAttributeString("ref", "Xcalibur");
writer.WriteEndElement(); // softwareRef
writer.WriteEndElement(); // instrumentConfiguration
writer.WriteEndElement(); // instrumentConfigurationList
writer.WriteStartElement("dataProcessingList");
writer.WriteAttributeString("count", "1");
writer.WriteStartElement("dataProcessing");
writer.WriteAttributeString("id", "ThermoRawFileParserProcessing");
writer.WriteStartElement("processingMethod");
writer.WriteAttributeString("order", "0");
writer.WriteAttributeString("softwareRef", "Monocle");
WriteCVParam("MS:1000544", "");
writer.WriteEndElement(); // processingMethod
writer.WriteEndElement(); // dataProcessing
writer.WriteEndElement(); // dataProcessingList
writer.WriteStartElement("run");
writer.WriteAttributeString("id", Path.GetFileNameWithoutExtension(header.FileName));
writer.WriteAttributeString("defaultInstrumentConfigurationRef", "IC1");
writer.WriteAttributeString("defaultSourceFileRef", "sourcefile_1");
writer.WriteStartElement("spectrumList");
writer.WriteAttributeString("count", header.ScanCount.ToString());
writer.WriteAttributeString("defaultDataProcessingRef", "ThermoRawFileParserProcessing");
}
/// <summary>
/// Run Monocle on the files indicated in the Processor
/// </summary>
public async void Run()
{
tokenSource = new CancellationTokenSource();
CancellationToken token = tokenSource.Token;
await Task.Run(() =>
{
token.ThrowIfCancellationRequested();
try
{
int filesCompleted = 0;
foreach (string newFile in files.FileList)
{
CurrentProgress = CalculateProgress(1, filesCompleted, files.FileList.Count);
TrackProcess(newFile, CurrentProgress, RunStatus.Started);
token.ThrowIfCancellationRequested();
IScanReader reader = ScanReaderFactory.GetReader(newFile);
reader.Open(newFile);
ScanFileHeader header = reader.GetHeader();
header.FileName = Path.GetFileName(newFile);
var Scans = new List <Monocle.Data.Scan>();
foreach (Scan scan in reader)
{
token.ThrowIfCancellationRequested();
Scans.Add(scan);
}
reader.Close();
CurrentProgress = CalculateProgress(2, filesCompleted, files.FileList.Count);
TrackProcess(newFile, CurrentProgress, RunStatus.Read);
token.ThrowIfCancellationRequested();
if (!ConvertOnly)
{
// Start Run across Scans
Monocle.Monocle.Run(ref Scans, monocleOptions);
CurrentProgress = CalculateProgress(3, filesCompleted, files.FileList.Count);
TrackProcess(newFile, CurrentProgress, RunStatus.Processed);
token.ThrowIfCancellationRequested();
}
string outputFilePath = Path.Combine(Path.GetDirectoryName(newFile), Path.GetFileNameWithoutExtension(newFile) +
"_monocle." +
monocleOptions.OutputFileType.ToString());
ScanWriterFactory.MakeTargetFileName(newFile, monocleOptions.OutputFileType);
IScanWriter writer = ScanWriterFactory.GetWriter(monocleOptions.OutputFileType);
writer.Open(outputFilePath);
writer.WriteHeader(header);
foreach (Scan scan in Scans)
{
token.ThrowIfCancellationRequested();
writer.WriteScan(scan);
}
writer.Close();
CurrentProgress = CalculateProgress(4, filesCompleted, files.FileList.Count);
TrackProcess(outputFilePath, CurrentProgress, RunStatus.Written);
token.ThrowIfCancellationRequested();
// Clear data
EmptyScans(Scans);
filesCompleted++;
CurrentProgress = CalculateProgress(4, filesCompleted, files.FileList.Count);
TrackProcess(outputFilePath, CurrentProgress, RunStatus.Finished);
}
AllFilesFinished(true);
}
catch (Exception ex)
{
Debug.WriteLine("File processing failed: " + ex);
}
});
}
/// <summary>
/// There is no place to store metadata in the csv file,
/// so calling this method does nothing.
/// </summary>
/// <param name="header"></param>
public void WriteHeader(ScanFileHeader header)
{
// Nothing to do.
}
