public List <IIdentifiedSpectrumBase> ReadFromFile(string filename)
{
if (!File.Exists(filename))
{
throw new FileNotFoundException("File not exist : " + filename);
}
var result = new List <IIdentifiedSpectrumBase>();
long fileSize = new FileInfo(filename).Length;
Progress.SetRange(0, fileSize);
char[] cs = new char[] { '\t' };
using (var br = new StreamReader(filename))
{
String line = br.ReadLine();
List <string> headers = line.Split(cs).ToList();
int seqIndex = headers.IndexOf("Sequence");
int refIndex = headers.IndexOf("Reference");
var seqConverter = new IdentifiedSpectrumSequenceConverter <IIdentifiedSpectrumBase>();
var refConverter = new IdentifiedSpectrumSequenceConverter <IIdentifiedSpectrumBase>();
while ((line = br.ReadLine()) != null)
{
if (0 == line.Trim().Length)
{
break;
}
string[] parts = line.Split(cs);
var item = new IdentifiedSpectrumBase();
seqConverter.SetProperty(item, parts[seqIndex]);
refConverter.SetProperty(item, parts[refIndex]);
item.SummaryLine = line;
result.Add(item);
}
}
return(result);
}
public void Test()
{
IPropertyConverter<IdentifiedSpectrum> io = new IdentifiedSpectrumSequenceConverter<IdentifiedSpectrum>();
var mph = new IdentifiedSpectrum();
var mp1 = new IdentifiedPeptide(mph);
mp1.Sequence = "AAAAA";
var mp2 = new IdentifiedPeptide(mph);
mp2.Sequence = "BBBBB";
Assert.AreEqual("Sequence", io.Name);
Assert.AreEqual("AAAAA ! BBBBB", io.GetProperty(mph));
io.SetProperty(mph, "CCCCC ! DDDDD ! EEEEE");
Assert.AreEqual(3, mph.Peptides.Count);
Assert.AreEqual("CCCCC", mph.Peptides[0].Sequence);
Assert.AreEqual("DDDDD", mph.Peptides[1].Sequence);
Assert.AreEqual("EEEEE", mph.Peptides[2].Sequence);
}
