public void WriteToFile(string proteinFile, IIdentifiedResult mr)
{
if (this.proteinConverter == null)
{
this.proteinConverter =
IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(
"Locus\tSequence Count\tSpectrum Count\tSequence Coverage\tLength\tMolWt\tpI\tValidation Status\tDescriptive Name",
'\t', "Dtaselect");
this.peptideConverter =
IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(
"Unique\tFileName\tScore\tDeltCN\tM+H+\tCalcM+H+\tTotalIntensity\tSpRank\tSpScore\tIonProportion\tRedundancy\tSequence",
'\t', "Dtaselect");
}
using (var sw = new StreamWriter(proteinFile))
{
sw.WriteLine("DTASelect v1.9");
sw.WriteLine();
sw.WriteLine("true Use criteria");
sw.WriteLine();
sw.WriteLine(this.proteinConverter.Name);
sw.WriteLine(this.peptideConverter.Name);
foreach (IdentifiedProteinGroup mpg in mr)
{
for (int proteinIndex = 0; proteinIndex < mpg.Count; proteinIndex++)
{
IIdentifiedProtein mpro = mpg[proteinIndex];
sw.WriteLine(this.proteinConverter.GetProperty(mpro));
}
mpg.GetSortedPeptides().ForEach(m => sw.WriteLine(this.peptideConverter.GetProperty(m)));
}
}
}
private void ResetSpectrumFactory()
{
var formatScore = StringUtils.GetDoubleFormat(this.ScoreDecimal);
var formatDiff = StringUtils.GetDoubleFormat(this.DiffDecimal);
var factory = IdentifiedSpectrumPropertyConverterFactory.GetInstance();
factory.InsertConverter(new IdentifiedSpectrumTheoreticalMinusExperimentalMassConverter <IIdentifiedSpectrum>(formatDiff));
factory.InsertConverter(new IdentifiedSpectrumScoreConverter <IIdentifiedSpectrum>(formatScore));
this.format.PeptideFormat.Factory = factory;
}
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);
}
public List <IIdentifiedSpectrum> ReadFromFile(string filename)
{
if (!File.Exists(filename))
{
throw new FileNotFoundException("File not exist : " + filename);
}
var result = new List <IIdentifiedSpectrum>();
long fileSize = new FileInfo(filename).Length;
Progress.SetRange(0, fileSize);
try
{
using (var br = new StreamReader(filename))
{
String line = br.ReadLine();
PeptideFormat = new LineFormat <IIdentifiedSpectrum>(IdentifiedSpectrumPropertyConverterFactory.GetInstance(),
line, "sequest");
while ((line = br.ReadLine()) != null)
{
if (0 == line.Trim().Length)
{
break;
}
Progress.SetPosition(br.BaseStream.Position);
result.Add(PeptideFormat.ParseString(line));
}
}
}
catch (Exception ex)
{
throw new Exception(MyConvert.Format("Reading from file {0} error :\n" + ex.Message, filename), ex);
}
string enzymeFile = filename + ".enzyme";
if (File.Exists(enzymeFile))
{
new ProteaseFile().Fill(enzymeFile, result);
}
return(result);
}
public O18QuantificationSummaryViewerUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
this.exportFile = new SaveFileArgument("O18 Quantification Result", "ProO18Quant");
InitializeSummaryFile();
var factory = IdentifiedSpectrumPropertyConverterFactory.GetInstance();
factory.InsertConverter(new IdentifiedSpectrumTheoreticalMinusExperimentalMassConverter <IIdentifiedSpectrum>("{0:0.000}"));
factory.InsertConverter(new IdentifiedSpectrumScoreConverter <IIdentifiedSpectrum>("{0:0}"));
this.format.PeptideFormat = new LineFormat <IIdentifiedSpectrum>(factory, "");
}
public IIdentifiedResult ReadFromFile(string proteinFile)
{
if (!File.Exists(proteinFile))
{
throw new FileNotFoundException("File not exist : " + proteinFile);
}
var result = new MascotResult();
var peptideMap = new Dictionary <string, IIdentifiedSpectrum>();
using (var filein = new StreamReader(proteinFile))
{
string lastLine;
while ((lastLine = filein.ReadLine()) != null)
{
if (lastLine.StartsWith("Locus"))
{
this.proteinConverter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(lastLine, '\t',
"Dtaselect");
}
if (lastLine.StartsWith("Unique"))
{
this.peptideConverter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(lastLine,
'\t',
"Dtaselect");
break;
}
}
IIdentifiedProteinGroup group;
lastLine = null;
while ((group = ReadNextProteinGroup(filein, peptideMap, ref lastLine)) != null)
{
result.Add(group);
}
}
return(result);
}
public SilacQuantificationSummaryViewerUI()
{
InitializeComponent();
Text = Constants.GetSQHTitle(title, version);
this.calc = new SilacProteinRatioCalculator();
this.option = new SilacQuantificationSummaryOption();
this.exportFile = new SaveFileArgument("SILAC Quantification Result", "ProSILACQuant");
InitializeSummaryFile();
var factory = IdentifiedSpectrumPropertyConverterFactory.GetInstance();
factory.InsertConverter(new IdentifiedSpectrumTheoreticalMinusExperimentalMassConverter <IIdentifiedSpectrum>("{0:0.000}"));
factory.InsertConverter(new IdentifiedSpectrumScoreConverter <IIdentifiedSpectrum>("{0:0}"));
this.format.PeptideFormat = new LineFormat <IIdentifiedSpectrum>(factory, "");
this.proteinRSquare.Box.TextChanged += ProteinRSquareChanged;
this.peptideRSquare.Box.TextChanged += PeptideRSquareChanged;
}
public override IEnumerable <string> Process(string fileName)
{
var ratioResult = fileName + ".dist";
using (StreamReader sr = new StreamReader(fileName))
using (StreamWriter sw = new StreamWriter(ratioResult))
{
var header = sr.ReadLine();
var peptideFormat = new LineFormat <IIdentifiedSpectrum>(IdentifiedSpectrumPropertyConverterFactory.GetInstance(), header, "mascot");
var spectrum = peptideFormat.ParseString(sr.ReadLine());
var itemList = spectrum.GetMaxQuantItemList();
sw.Write("Peptide");
foreach (var func in funcs)
{
foreach (var item in itemList)
{
sw.Write("\t" + func.Name + ' ' + item.Name);
}
}
sw.WriteLine();
while (spectrum != null)
{
var curItem = spectrum.GetMaxQuantItemList();
if (curItem.QuantifiedExperimentCount >= minCount)
{
StringBuilder sb = new StringBuilder(spectrum.Peptide.Sequence);
bool bHasValue = false;
foreach (var func in funcs)
{
foreach (var item in curItem)
{
var value = func.ItemFunc(item);
if (value == string.Empty)
{
sb.Append("\tNA");
}
else
{
bHasValue = true;
sb.AppendFormat("\t{0}", value);
}
}
}
if (bHasValue)
{
sw.WriteLine(sb.ToString());
}
}
string line = sr.ReadLine();
if (line == null)
{
break;
}
spectrum = peptideFormat.ParseString(line);
}
return(new[] { ratioResult });
}
}
public SequestPeptideTextFormat(string header)
{
this.PeptideFormat = new LineFormat <IIdentifiedSpectrum>(
IdentifiedSpectrumPropertyConverterFactory.GetInstance(), header, "sequest");
}
public SequestPeptideTextFormat()
{
this.PeptideFormat = new LineFormat <IIdentifiedSpectrum>(
IdentifiedSpectrumPropertyConverterFactory.GetInstance(), SequestHeader.SEQUEST_PEPTIDE_HEADER, "sequest");
}