public List <IsosResult> getIsosResults(string isosInputFile, DeconTools.Backend.Globals.MSFileType filetype)
{
var isoutil = new IsosResultUtilities();
isoutil.LoadResults(isosInputFile, filetype);
return(isoutil.Results);
}
public List <IsosResult> getIsosResults(string isosInputFile, DeconTools.Backend.Globals.MSFileType filetype, int minScan, int maxScan)
{
var isoutil = new IsosResultUtilities();
isoutil.LoadResults(isosInputFile, filetype);
return(isoutil.Results.Where(p => p.ScanSet.PrimaryScanNumber >= minScan && p.ScanSet.PrimaryScanNumber <= maxScan).ToList());
}
private List <IsosResult> readInIsos(string canonIsosFilename, DeconTools.Backend.Globals.MSFileType filetype)
{
List <IsosResult> results = new List <IsosResult>();
IsosImporter importer = new IsosImporter(canonIsosFilename, filetype);
importer.Import(results);
return(results);
}
public IsosImporter(string importFilename, DeconTools.Backend.Globals.MSFileType filetype)
{
this.importFilename = importFilename;
this.delimiter = ',';
this.fileType = filetype;
this.minVal = int.MinValue;
this.maxVal = int.MaxValue;
try
{
this.reader = new StreamReader(importFilename);
}
catch (Exception)
{
throw new System.IO.IOException("There was a problem reading the _isos data file\n");
}
}
public IsosImporter(string importFilename, DeconTools.Backend.Globals.MSFileType filetype, int minValue, int maxValue)
: this(importFilename, filetype)
{
this.minVal = minValue;
this.maxVal = maxValue;
}
private Run getRunFromIsosFilename(string p, DeconTools.Backend.Globals.MSFileType filetype)
{
var runFilename = p.Replace("_isos", "");
var replacementExtension = "";
switch (filetype)
{
case Globals.MSFileType.Undefined:
break;
case Globals.MSFileType.Agilent_WIFF:
replacementExtension = ".WIFF";
break;
case Globals.MSFileType.Agilent_D:
replacementExtension = ".D";
break;
case Globals.MSFileType.Ascii:
break;
case Globals.MSFileType.Bruker:
break;
case Globals.MSFileType.Bruker_Ascii:
break;
case Globals.MSFileType.Finnigan:
replacementExtension = ".RAW";
break;
case Globals.MSFileType.ICR2LS_Rawdata:
break;
case Globals.MSFileType.Micromass_Rawdata:
break;
case Globals.MSFileType.MZXML_Rawdata:
break;
case Globals.MSFileType.PNNL_IMS:
replacementExtension = ".IMF";
break;
case Globals.MSFileType.PNNL_UIMF:
replacementExtension = ".UIMF";
break;
case Globals.MSFileType.SUNEXTREL:
break;
default:
replacementExtension = ".undefined";
break;
}
runFilename.Replace(".csv", replacementExtension);
var factory = new RunFactory();
Run run;
try
{
run = factory.CreateRun(runFilename);
}
catch (Exception)
{
run = null;
}
return(run);
}
private Globals.MSFileType guessFileTypeFromFileName(string filename)
{
RunFactory runFactory = new RunFactory();
Run run = runFactory.CreateRun(filename);
if (run != null)
{
DeconTools.Backend.Globals.MSFileType filetype = run.MSFileType;
run.Dispose();
return(filetype);
}
try
{
if (Directory.Exists(filename))
{
if (filename.EndsWith(".d", StringComparison.OrdinalIgnoreCase))
{
return(Globals.MSFileType.Agilent_D);
}
}
if (!File.Exists(filename))
{
return(Globals.MSFileType.Undefined);
}
string extension = Path.GetExtension(filename);
if (extension == null)
{
return(Globals.MSFileType.Undefined);
}
switch (extension.ToLower())
{
case ".d":
return(Globals.MSFileType.Agilent_D);
case ".raw":
return(Globals.MSFileType.Finnigan);
case ".imf":
return(Globals.MSFileType.PNNL_IMS);
case ".uimf":
return(Globals.MSFileType.PNNL_UIMF);
case ".mzxml":
return(Globals.MSFileType.MZXML_Rawdata);
// Deprecated in February 2017
// case ".yafms":
// return Globals.MSFileType.YAFMS;
default:
var fileName = Path.GetFileName(filename);
if (fileName != null && fileName.ToLower() == "acqus")
{
return(Globals.MSFileType.Bruker);
}
break;
}
return(Globals.MSFileType.Undefined);
}
catch (Exception)
{
return(Globals.MSFileType.Undefined);
}
}
