public void TestDtaOutZipFile() { var file = new DtaOutFilenameConverter("d.e.c.zip"); Assert.IsTrue(file.IsZip); Assert.IsFalse(file.IsDtasOutsFile); Assert.AreEqual("d.e.c", file.PureName); Assert.AreEqual("d.e.c.zip", file.GetDtasFilename()); Assert.AreEqual("d.e.c.zip", file.GetOutsFilename()); }
private void InitDtasFilePathMap(List <string> dtasFiles) { filePathMap = new Dictionary <string, List <string> >(); foreach (string dtasFile in dtasFiles) { string name = new DtaOutFilenameConverter(new FileInfo(dtasFile).Name).PureName; if (!filePathMap.ContainsKey(name)) { filePathMap[name] = new List <string>(); } filePathMap[name].Add(dtasFile); } }
private void ExtractMultipleRaw(string raw, List <string> rawFiles, List <IIdentifiedSpectrum> peptides) { string toDirectory = CreateToDirectory(raw); List <string> dtaFilenames = GetDtaFilenames(peptides); string dtasFile = new DtaOutFilenameConverter(rawFiles[0]).GetDtasFilename(); using (DtasReader dtas = new DtasReader(dtasFile)) { Progress.SetMessage(0, "Extracting from " + dtasFile + " ..."); ExtractFile(dtas, dtaFilenames, toDirectory); } Dictionary <string, IIdentifiedSpectrum> outFilenamePeptideMap = GetOutFilenamePeptideMap(peptides); foreach (string rawFile in rawFiles) { string outsFile = new DtaOutFilenameConverter(rawFiles[0]).GetOutsFilename(); Progress.SetMessage(0, "Extracting from " + outsFile + " ..."); using (OutsReader outs = new OutsReader(outsFile)) { ExtractFileByPeptide(outs, outFilenamePeptideMap, toDirectory); } } if (outFilenamePeptideMap.Count > 0) { StringBuilder sb; if (outFilenamePeptideMap.Count == 1) { sb = new StringBuilder("There is a file not found in dtas/outs file"); } else { sb = new StringBuilder("There are a few files not found in dtas/outs file"); } foreach (string key in outFilenamePeptideMap.Keys) { sb.Append("\n" + key); } throw new Exception(sb.ToString()); } }
private void ExtractSingleRaw(string raw, string rawFile, List <IIdentifiedSpectrum> peptides) { string toDirectory = CreateToDirectory(raw); List <string> dtaFilenames = GetDtaFilenames(peptides); string dtasFile = new DtaOutFilenameConverter(rawFile).GetDtasFilename(); using (DtasReader dtas = new DtasReader(dtasFile)) { Progress.SetMessage(0, MyConvert.Format("Extracting dta from {0} ...", dtasFile)); ExtractFile(dtas, dtaFilenames, toDirectory); } List <string> outFilenames = GetOutFilenames(peptides); string outsFile = new DtaOutFilenameConverter(rawFile).GetOutsFilename(); using (OutsReader outs = new OutsReader(outsFile)) { Progress.SetMessage(0, MyConvert.Format("Extracting out from {0} ...", outsFile)); ExtractFile(outs, outFilenames, toDirectory); } }