Exemplo n.º 1
0
        /// <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
        }
Exemplo n.º 2
0
        /// <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
        }
Exemplo n.º 3
0
        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);
        }
Exemplo n.º 4
0
        /// <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();
        }
Exemplo n.º 5
0
        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);
        }
Exemplo n.º 6
0
        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");
        }
Exemplo n.º 7
0
        /// <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);
                }
            });
        }
Exemplo n.º 8
0
 /// <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.
 }