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);
}
}
