private void InitLabelFormat(List <string> headers)
{
string sline = string.Empty;
foreach (string header in headers)
{
if (header.StartsWith("H PLINE"))
{
this.proteinFormat = new LineFormat <CensusProteinItem>(CensusProteinItemPropertyConverterFactory.GetInstance(), header.Substring(2));
}
else if (header.StartsWith("H SLINE"))
{
sline = header.Substring(2).Trim();
this.peptideFormat = new LineFormat <CensusPeptideItem>(CensusPeptideItemPropertyConverterFactory.GetInstance(), sline);
}
else if (header.StartsWith("H &SLINE"))
{
string line = header.Substring(3).Trim();
if (line.Equals(sline))
{
continue;
}
if (line.Length > sline.Length)
{
this.peptideFormat = new LineFormat <CensusPeptideItem>(CensusPeptideItemPropertyConverterFactory.GetInstance(), line);
}
}
}
}
public static CensusPeptideItemPropertyConverterFactory GetInstance()
{
if (instance == null)
{
instance = new CensusPeptideItemPropertyConverterFactory();
instance.RegisterConverter(new CensusPeptideItem_UNIQUE_Converter());
instance.RegisterConverter(new CensusPeptideItem_SEQUENCE_Converter());
IPropertyConverter <CensusPeptideItem> ratioConverter = new CensusPeptideItem_RATIO_Converter();
instance.RegisterConverter(ratioConverter);
instance.RegisterConverter(new CensusPeptideItem_REGRESSION_FACTOR_Converter());
instance.RegisterConverter(new CensusPeptideItem_DETERMINANT_FACTOR_Converter());
IPropertyConverter <CensusPeptideItem> samIntConverter = new CensusPeptideItem_SAM_INT_Converter();
instance.RegisterConverter(samIntConverter);
IPropertyConverter <CensusPeptideItem> refIntConverter = new CensusPeptideItem_REF_INT_Converter();
instance.RegisterConverter(refIntConverter);
instance.RegisterConverter(new CensusPeptideItem_AREA_RATIO_Converter());
instance.RegisterConverter(new CensusPeptideItem_PROFILE_SCORE_Converter());
instance.RegisterConverter(new CensusPeptideItem_FILE_NAME_Converter());
instance.RegisterConverter(new CensusPeptideItem_SCAN_Converter());
}
return(instance);
}
private void InitDefaultFormat()
{
this.proteinFormat = new LineFormat <CensusProteinItem>(
CensusProteinItemPropertyConverterFactory.GetInstance(),
"PLINE LOCUS AVERAGE_RATIO STANDARD_DEVIATION WEIGHTED_AVERAGE PEPTIDE_NUM SPEC_COUNT DESCRIPTION");
this.peptideFormat = new LineFormat <CensusPeptideItem>(
CensusPeptideItemPropertyConverterFactory.GetInstance(),
"SLINE UNIQUE SEQUENCE RATIO REGRESSION_FACTOR DETERMINANT_FACTOR XCorr deltaCN SAM_INT REF_INT AREA_RATIO SINGLETON_SCORE FILE_NAME");
}
private void InitLabelFreeFormat(List <string> headers)
{
Regex proteinReg = new Regex(@"AVG\((\S+)_INT/(\S+)_INT\)");
string sampleName = "";
string referenceName = "";
foreach (string header in headers)
{
if (header.StartsWith("H PLINE"))
{
Match m = proteinReg.Match(header);
sampleName = m.Groups[1].Value;
referenceName = m.Groups[2].Value;
CensusProteinItemPropertyConverterFactory factory = CensusProteinItemPropertyConverterFactory.GetInstance();
IPropertyConverter <CensusProteinItem> averageRatioConverter = new CensusProteinItem_AVERAGE_RATIO_Converter();
factory.RegisterConverter(new PropertyAliasConverter <CensusProteinItem>(averageRatioConverter, MyConvert.Format("AVG({0}_INT/{1}_INT)", sampleName, referenceName)));
IPropertyConverter <CensusProteinItem> sdConverter = new CensusProteinItem_STANDARD_DEVIATION_Converter();
factory.RegisterConverter(new PropertyAliasConverter <CensusProteinItem>(sdConverter, MyConvert.Format("STDEV({0}_INT/{1}_INT)", sampleName, referenceName)));
this.proteinFormat = new LineFormat <CensusProteinItem>(factory, header.Substring(2));
}
else if (header.StartsWith("H SLINE"))
{
string peptideHeader = header.Substring(2);
List <string> parts = new List <string>(peptideHeader.Split(new char[] { '\t' }));
parts.Remove(MyConvert.Format("SPEC_COUNT({0})", sampleName));
parts.Remove(MyConvert.Format("SPEC_COUNT({0})", referenceName));
peptideHeader = StringUtils.Merge(parts, "\t");
CensusPeptideItemPropertyConverterFactory factory = CensusPeptideItemPropertyConverterFactory.GetInstance();
IPropertyConverter <CensusPeptideItem> ratioConverter = new CensusPeptideItem_RATIO_Converter();
factory.RegisterConverter(new PropertyAliasConverter <CensusPeptideItem>(ratioConverter, MyConvert.Format("{0}_INT/{1}_INT", sampleName, referenceName)));
IPropertyConverter <CensusPeptideItem> samIntConverter = new CensusPeptideItem_SAM_INT_Converter();
factory.RegisterConverter(new PropertyAliasConverter <CensusPeptideItem>(samIntConverter, MyConvert.Format("INT({0})", sampleName)));
IPropertyConverter <CensusPeptideItem> refIntConverter = new CensusPeptideItem_REF_INT_Converter();
factory.RegisterConverter(new PropertyAliasConverter <CensusPeptideItem>(refIntConverter, MyConvert.Format("INT({0})", referenceName)));
this.peptideFormat = new LineFormat <CensusPeptideItem>(factory, peptideHeader);
}
}
}