public IonDefinitionItem(IsobaricType plexType, double mass)
{
this.PlexType = plexType;
this.Mass = mass;
this.Index = (int)(Math.Round(mass));
this.Name = "I" + Index.ToString();
}
public List <IsobaricIndex> GetSamples(IsobaricType sampleType)
{
var result = sampleType.GetFuncs();
result.RemoveAll(m => References.Any(n => n.Name.Equals(m.Name)));
return(result);
}
public ITraqResultMultipleFileDistiller(IITraqRawReader reader, string[] rawFiles, bool individual, int minPeakCount, IsobaricType plexType, string isotopeImpurityCorrectionTableFileName, IITraqNormalizationBuilder builder, double precursorPPMTolearnce)
{
this.reader = reader;
this.rawFiles = rawFiles;
this.individual = individual;
this.minPeakCount = minPeakCount;
this.plexType = plexType;
this.isotopeImpurityCorrectionTableFileName = isotopeImpurityCorrectionTableFileName;
this.builder = builder;
this.precursorPPMTolearnce = precursorPPMTolearnce;
}
private void CheckPlexType(IsobaricType plexType, string expectHeader, string expectValue)
{
var ann = new IdentifiedSpectrum();
var pqr = new IsobaricItem()
{
PlexType = plexType,
Valid = true,
ValidProbability = 0.0005
};
var refItems = plexType.GetDefinition().Items;
foreach (var item in refItems)
{
pqr[item.Index] = item.Mass;
}
ann.SetIsobaricItem(pqr);
//从实例构建converter
var converter = new ITraqItemPlexConverter <IAnnotation>();
List <IPropertyConverter <IAnnotation> > converters = new List <IPropertyConverter <IAnnotation> >();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter <IAnnotation> finalConverter = new CompositePropertyConverter <IAnnotation>(converters, ',');
if (exportToConsole)
{
Console.WriteLine(finalConverter.Name);
}
Assert.AreEqual(expectHeader, finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
if (exportToConsole)
{
Console.WriteLine(line1);
}
Assert.AreEqual(expectValue, line1);
var protein2 = new IdentifiedSpectrum();
//从factory根据header构建converter
var finalC = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
private void CheckPlexType(IsobaricType plexType, string expectHeader, string expectValue)
{
var ann = new IdentifiedSpectrum();
var pqr = new IsobaricItem()
{
PlexType = plexType,
Valid = true,
ValidProbability = 0.0005
};
var refItems = plexType.GetDefinition().Items;
foreach (var item in refItems)
{
pqr[item.Index] = item.Mass;
}
ann.SetIsobaricItem(pqr);
//从实例构建converter
var converter = new ITraqItemPlexConverter<IAnnotation>();
List<IPropertyConverter<IAnnotation>> converters = new List<IPropertyConverter<IAnnotation>>();
converters.Add(converter);
converters.AddRange(converter.GetRelativeConverter(new IAnnotation[] { ann }.ToList()));
CompositePropertyConverter<IAnnotation> finalConverter = new CompositePropertyConverter<IAnnotation>(converters, ',');
if (exportToConsole)
{
Console.WriteLine(finalConverter.Name);
}
Assert.AreEqual(expectHeader, finalConverter.Name);
var line1 = finalConverter.GetProperty(ann);
if (exportToConsole)
{
Console.WriteLine(line1);
}
Assert.AreEqual(expectValue, line1);
var protein2 = new IdentifiedSpectrum();
//从factory根据header构建converter
var finalC = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(finalConverter.Name, ',');
finalC.SetProperty(protein2, line1);
var line2 = finalConverter.GetProperty(protein2);
Assert.AreEqual(line1, line2);
}
//private static readonly IonDefinitionItem[] _TMTPlex10 = new IonDefinitionItem[]{
// new IonDefinitionItem(IsobaricType.TMT10,126.127726),
// new IonDefinitionItem(IsobaricType.TMT10,127.124761),
// new IonDefinitionItem(IsobaricType.TMT10,127.131081),
// new IonDefinitionItem(IsobaricType.TMT10,128.128116),
// new IonDefinitionItem(IsobaricType.TMT10,128.134436),
// new IonDefinitionItem(IsobaricType.TMT10,129.131471),
// new IonDefinitionItem(IsobaricType.TMT10,129.13779),
// new IonDefinitionItem(IsobaricType.TMT10,130.134825),
// new IonDefinitionItem(IsobaricType.TMT10,130.141145),
// new IonDefinitionItem(IsobaricType.TMT10,131.13818)
//};
//public static readonly IsobaricDefinition TMTPlex10 = new IsobaricDefinition(_TMTPlex10)
//{
// TagMass = new double[] { 230.1699 }
//};
public static IsobaricDefinition GetDefinition(this IsobaricType plexType)
{
if (plexType == IsobaricType.PLEX4)
{
return(ITraqPlex4);
}
if (plexType == IsobaricType.PLEX8)
{
return(ITraqPlex8);
}
if (plexType == IsobaricType.TMT6)
{
return(TMTPlex6);
}
//if (plexType == IsobaricType.TMT10)
//{
// return TMTPlex10;
//}
throw new ArgumentException("Unknown isobaric type : " + plexType.ToString());
}
public ITraqItemBaseConverter(string name, Func <IsobaricItem, string> getValue, Action <IsobaricItem, string> setValue, IsobaricType plexType, bool setPlexType)
: this(name, getValue, setValue)
{
this.plexType = plexType;
this.setPlexType = setPlexType;
}
public static List <IsobaricIndex> GetFuncs(this IsobaricType plexType)
{
return((from item in plexType.GetDefinition().Items
select new IsobaricIndex(item.Index)).ToList());
}
public static IsobaricItemImpl CreateItem(this IsobaricType plexType, IsobaricItem parent)
{
return(new IsobaricItemImpl(parent, plexType.GetDefinition()));
}
public static double[][] ParseTable(IsobaricType plexType, string isotopeImpurityFile)
{
var definition = plexType.GetDefinition();
var items = definition.Items;
string[] lines = File.ReadAllLines(isotopeImpurityFile);
if (lines.Length < items.Length + 1)
{
throw new ArgumentException(string.Format("Wrong format of Isotope Impurity Correction Table File of {0}\n{1}", plexType, isotopeImpurityFile));
}
//Skip the header line
lines = lines.Skip(1).ToArray();
char splitChar;
if (lines[0].Contains(','))
{
splitChar = ',';
}
else
{
splitChar = '\t';
}
//Each line should contain reagent name and five values (-2,-1,0,1,2)
lines = (from l in lines
let s = l.Trim().Split(splitChar)
where s.Length == 6
select l.Trim()).ToArray();
if (lines.Length != items.Length)
{
throw new ArgumentException(string.Format("Length not equals between plex type {0} and impurity file {1}", plexType, isotopeImpurityFile));
}
var ignore = new List <int>();
for (int i = definition.MaxIndex - 1; i > definition.MinIndex; i--)
{
if (!definition.IsValid(i))
{
ignore.Add(i - definition.MinIndex);
}
}
int len = definition.MaxIndex - definition.MinIndex + 1;
Dictionary <int, double[]> dic = new Dictionary <int, double[]>();
int index = definition.MinIndex - 1;
for (int i = 0; i < items.Length; i++)
{
var lst = new List <double>();
for (int j = 0; j < len; j++)
{
lst.Add(0);
}
var p = GetIsotopes(lines[i], splitChar, ref index);
var startPos = items[i].Index - definition.MinIndex - 2;
var endPos = Math.Min(len, startPos + 5);
var fromPos = Math.Max(0, startPos);
for (int j = fromPos; j < endPos; j++)
{
var pIndex = j - startPos;
lst[j] = p[pIndex];
}
foreach (var ign in ignore)
{
lst.RemoveAt(ign);
}
dic[index] = lst.ToArray();
}
return((from key in dic.Keys
orderby key
select dic[key]).ToArray());
}
public IsobaricImpurityCorrectionCalculator(IsobaricType plexType, string isotopeImpurityCorrectionTableFileName)
{
this.PlexType = plexType;
this.plexTable = ParseTable(plexType, isotopeImpurityCorrectionTableFileName);
}
public ITraqResultFileDistiller(IITraqRawReader itraqReader, int minPeakCount, IsobaricType plexType, string isotopeImpurityFile, double precursorPPM)
{
this.itraqReader = itraqReader;
this.minPeakCount = minPeakCount;
this.calc = new IsobaricImpurityCorrectionCalculator(plexType, isotopeImpurityFile);
this.precursorPPM = precursorPPM;
}
