private IIdentifiedResultTextFormat GetMultipleFileFormat(IIdentifiedSpectrumWriter writer)
{
var result = DoGetMultipleFileFormat();
result.ProteinFormat = format.ProteinFormat.GetLineFormat(proteinColumns.Merge("\t"));
result.PeptideFormat = format.PeptideFormat.GetLineFormat(peptideColumns.Where(m => !string.IsNullOrWhiteSpace(m)).Merge("\t"));
result.ScanWriter = writer;
return(result);
}
private IIdentifiedResultTextFormat GetSingleFileFormat(IIdentifiedSpectrumWriter writer)
{
QuantificationResultSingleFileFormat result = new QuantificationResultSingleFileFormat()
{
ScanWriter = writer,
};
result.ProteinFormat = format.ProteinFormat.GetLineFormat(proteinColumns.Merge("\t"));
result.PeptideFormat = format.PeptideFormat.GetLineFormat(peptideColumns.Merge("\t"));
return(result);
}
protected virtual IFileWriter <IIdentifiedResult> GetExportFileWriter()
{
QuantificationExportForm form = new QuantificationExportForm();
form.ConfigFileName = GetExportConfigFileName();
IIdentifiedSpectrumWriter writer = GetScanWriter("");
var allheaders = (from h in writer.Header.Split('\t')
where !string.IsNullOrWhiteSpace(h)
select h).ToList();
form.InitializeScan(allheaders, ExportScanHeaders);
if (form.MyShowDialog(this) != DialogResult.OK)
{
return(null);
}
form.SaveOption();
if (form.IsExportScan)
{
var detailDir = new FileInfo(summaryFilename).DirectoryName + "/" + GetDetailDirectoryName();
ExportScanHeaders = form.GetCheckedScanHeaders();
writer = GetScanWriter(detailDir, ExportScanHeaders.Merge("\t"));
}
else
{
writer = null;
}
IIdentifiedResultTextFormat result;
if (form.IsSingleFile)
{
result = GetSingleFileFormat(writer);
}
else
{
result = GetMultipleFileFormat(writer);
}
IIdentifiedProteinGroupWriter groupWriter;
if (form.IsFilterProteinName)
{
string[] parts = form.ProteinNamePattern.Split(';');
List <string> patterns = new List <string>();
foreach (string part in parts)
{
if (part.Trim().Length > 0)
{
patterns.Add(part.Trim());
}
}
groupWriter = new IdentifiedProteinGroupSingleLineWriter(patterns.ToArray());
}
else
{
groupWriter = new IdentifiedProteinGroupMultipleLineWriter();
}
result.GroupWriter = groupWriter;
result.ValidGroup = (m => m[0].IsEnabled(true) && option.IsProteinRatioValid(m[0]) && !option.IsProteinOutlier(m[0]));
result.ValidSpectrum = (m => m.IsEnabled(true) && option.IsPeptideRatioValid(m) && !option.IsPeptideOutlier(m));
return(result);
}