protected string GetRatioFile(IQuantificationSummaryOption option, IIdentifiedSpectrum mph)
{
string ratioFile = mph.GetQuantificationItem().Filename;
if (ratioFile.Equals("-"))
{
return(null);
}
FileInfo fi = new FileInfo(SummaryFilename);
string result;
if (IsRelativeDir(ratioFile))
{
result = fi.DirectoryName + "/" + ratioFile;
}
else
{
result = fi.DirectoryName + "/" + DefaultDetailDirectory + "/" + ratioFile;
}
result = new FileInfo(result).FullName;
if (!File.Exists(result))
{
return(null);
}
return(result);
}
protected virtual string GetRatioFile(IIdentifiedSpectrum mph)
{
string ratioFile;
if (mph.GetQuantificationItem() != null)
{
ratioFile = mph.GetQuantificationItem().Filename;
}
else
{
ratioFile = (string)mph.Annotations[option.RatioFileKey];
}
if (string.IsNullOrEmpty(ratioFile) || ratioFile.Equals("-"))
{
return(null);
}
FileInfo fi = new FileInfo(summaryFilename);
string result;
if (IsRelativeDir(ratioFile))
{
result = fi.DirectoryName + "/" + ratioFile;
}
else
{
result = fi.DirectoryName + "/" + GetDetailDirectoryName() + "/" + ratioFile;
}
result = new FileInfo(result).FullName;
if (!File.Exists(result))
{
MessageBox.Show(this, "Cannot find file " + result, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return(null);
}
return(result);
}
public void WriteToStream(System.IO.StreamWriter sw, IIdentifiedSpectrum peptide)
{
string detailFile = this.detailDirectory + "\\" + peptide.GetQuantificationItem().Filename;
if (File.Exists(detailFile))
{
SilacQuantificationSummaryItem item = format.ReadFromFile(detailFile);
Func <SilacPeakListPair, double> SampleIntensityFunc;
Func <SilacPeakListPair, double> ReferenceIntensityFunc;
if (item.SampleIsLight)
{
SampleIntensityFunc = m => m.LightIntensity;
ReferenceIntensityFunc = m => m.HeavyIntensity;
}
else
{
SampleIntensityFunc = m => m.HeavyIntensity;
ReferenceIntensityFunc = m => m.LightIntensity;
}
var valueFuncs = new List <Func <SilacPeakListPair, string> >();
foreach (var header in headers)
{
switch (header)
{
case "Scan": valueFuncs.Add(m => string.Format("{0}", m.Scan));
break;
case "Retentiontime": valueFuncs.Add(m => string.Format("{0:0.00}", m.Light.ScanTimes[0].RetentionTime));
break;
case "Identified": valueFuncs.Add(m => m.IsIdentified.ToString());
break;
case QuantificationItem.KEY_REFERENCE_INTENSITY: valueFuncs.Add(m => string.Format("{0:0.0}", ReferenceIntensityFunc(m)));
break;
case QuantificationItem.KEY_SAMPLE_INTENSITY: valueFuncs.Add(m => string.Format("{0:0.0}", SampleIntensityFunc(m)));
break;
case QuantificationItem.KEY_RATIO: valueFuncs.Add(m => string.Format("{0:0.0000}", SampleIntensityFunc(m) / ReferenceIntensityFunc(m)));
break;
case "Protein": valueFuncs.Add(m => peptide.GetProteins("/"));
break;
}
;
}
foreach (var scan in item.ObservedEnvelopes)
{
if (scan.Enabled)
{
var ri = ReferenceIntensityFunc(scan);
var si = SampleIntensityFunc(scan);
if (ri == 0.0 || si == 0.0)
{
continue;
}
sw.Write("\t");
foreach (var func in valueFuncs)
{
sw.Write("\t{0}", func(scan));
}
sw.WriteLine();
}
}
}
}
public double CalculatePeptideRatio(IIdentifiedSpectrum spectrum)
{
return(spectrum.GetQuantificationItem().Ratio);
}
public bool HasPeptideRatio(IIdentifiedSpectrum spectrum)
{
return(spectrum.GetQuantificationItem() != null);
}
