public override IsobaricResult ReadFromFile(string fileName)
{
IsobaricResult result = new IsobaricResult();
result.PlexType = IsobaricScanXmlUtils.GetIsobaricType(fileName);
result.UsedChannels = IsobaricScanXmlUtils.GetUsedChannels(fileName, result.PlexType);
result.Comments = IsobaricScanXmlUtils.GetComments(fileName);
using (var reader = new IsobaricResultXmlFormatReader())
{
reader.Progress = this.Progress;
reader.ReadReporters = this.HasReporters && result.UsedChannels != null;
reader.ReadPeaks = this.ReadPeaks;
reader.Accept = this.Accept;
reader.OpenFile(fileName);
IsobaricScan item;
while (null != (item = reader.Next(result.UsedChannels)))
{
result.Add(item);
}
}
return(result);
}
private List <IsobaricIndex> GetReferenceFuncs()
{
var usedChannels = IsobaricScanXmlUtils.GetUsedChannels(iTraqFile.FullName);
var result = refChannels.GetFuncs();
foreach (var refFunc in result)
{
bool bFound = false;
for (int i = 0; i < usedChannels.Count; i++)
{
if (usedChannels[i].Name.Equals(refFunc.Name))
{
refFunc.Index = i;
bFound = true;
break;
}
}
if (!bFound)
{
throw new Exception(string.Format("Channel {0} was not used in sample and cannot be used as reference, valid channels are {1}",
refFunc.Name,
usedChannels.ConvertAll(l => l.Name).Merge("/")));
}
}
return(result);
}
protected IsobaricLabelingExperimentalDesign GetStatisticOption()
{
var option = new IsobaricLabelingExperimentalDesign();
option.DatasetMap = pnlClassification.GetClassificationSet();
option.IsobaricFile = iTraqFile.FullName;
option.References = GetReferenceFuncs();
option.PlexType = IsobaricScanXmlUtils.GetIsobaricType(txtIsobaricXmlFile.Text);
return(option);
}
private void txtXmlFile_TextChanged(object sender, EventArgs e)
{
if (File.Exists(txtIsobaricXmlFile.Text))
{
try
{
refChannels.PlexType = IsobaricScanXmlUtils.GetIsobaricType(txtIsobaricXmlFile.Text);
}
catch (Exception ex)
{
MessageBox.Show(this, string.Format("Failed to get isobaric type from {0}, error: {1}", txtIsobaricXmlFile.Text, ex.Message));
}
}
}
public List <IsobaricIndex> GetSamples()
{
var result = new List <IsobaricIndex>();
var used = IsobaricScanXmlUtils.GetUsedChannels(this.IsobaricFile);
for (int i = 0; i < used.Count; i++)
{
var channel = used[i];
if (References.Any(m => m.Name.Equals(channel.Name)))
{
continue;
}
result.Add(new IsobaricIndex(used[i].Name, i));
}
return(result);
}
/// <summary>
/// 从isobaricFile中读取spectra对应的isobaric labelling信息。
/// </summary>
/// <param name="spectra"></param>
/// <param name="isobaricFile"></param>
/// <param name="progress"></param>
public static void Load(List <IIdentifiedSpectrum> spectra, string isobaricFile, bool readPeaks = false, IProgressCallback progress = null)
{
if (progress == null)
{
progress = new EmptyProgressCallback();
}
var fileNames = new HashSet <string>(from s in spectra
let fs = s.Query.FileScan
select fs.Experimental + "," + fs.FirstScan.ToString());
using (var reader = IsobaricResultFileFormatFactory.GetXmlReader(true, readPeaks))
{
var usedChannels = IsobaricScanXmlUtils.GetUsedChannels(isobaricFile);
reader.Open(isobaricFile);
progress.SetMessage("Reading Isobaric from {0} ...", isobaricFile);
progress.SetRange(1, spectra.Count);
foreach (var spectrum in spectra)
{
if (progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
progress.Increment(1);
var fs = spectrum.Query.FileScan;
if (reader.Has(fs.Experimental, fs.FirstScan))
{
spectrum.SetIsobaricItem(reader.Read(fs.Experimental, fs.FirstScan, usedChannels));
}
else
{
spectrum.SetIsobaricItem(null);
}
}
}
}
public IsobaricScan Next(List <UsedChannel> used)
{
Progress.SetPosition(_stream.Position);
return(IsobaricScanXmlUtils.Parse(_reader, used, ReadReporters, ReadPeaks, Accept, true));
}
public IsobaricScan Read(string experimental, int scan, List <UsedChannel> used)
{
var xml = ReadXmlBytes(experimental, scan);
return(IsobaricScanXmlUtils.Parse(xml, used, this.ReadReporters, this.ReadPeaks, this.Accept));
}
