public void Load(XElement parentNode)
{
XElement xml = parentNode.Element("FalseDiscoveryRate");
FilterByFdr = Convert.ToBoolean(xml.Element("Filtered").Value);
FdrLevel = (FalseDiscoveryRateLevel)Enum.Parse(FalseDiscoveryRateLevel.Peptide.GetType(), xml.GetChildValue("Level", FalseDiscoveryRateLevel.Peptide.ToString()));
MaxPeptideFdr = MyConvert.ToDouble(xml.Element("MaxPeptideFdr").Value);
FdrPeptideCount = Convert.ToInt32(xml.Element("FdrPeptideCount").Value);
FdrType = (FalseDiscoveryRateType)Enum.Parse(FalseDiscoveryRateType.Total.GetType(), xml.GetChildValue("Type", FalseDiscoveryRateType.Total.ToString()));
FdrValue = MyConvert.ToDouble(xml.Element("Value").Value);
if (xml.Element("TargetDecoyConflictType") != null)
{
TargetDecoyConflictType = ResolveTargetDecoyConflictTypeFactory.Find(xml.Element("TargetDecoyConflictType").Value);
}
if (xml.Element("FilterOneHitWonder") != null)
{
FilterOneHitWonder = bool.Parse(xml.Element("FilterOneHitWonder").Value);
}
else
{
FilterOneHitWonder = false;
}
if (xml.Element("MinOneHitWonderPeptideCount") != null)
{
MinOneHitWonderPeptideCount = int.Parse(xml.Element("MinOneHitWonderPeptideCount").Value);
}
else
{
MinOneHitWonderPeptideCount = 2;
}
if (xml.Element("ByDecoySpectra") != null)
{
ByDecoySpectra = bool.Parse(xml.Element("ByDecoySpectra").Value);
}
else
{
ByDecoySpectra = false;
}
if (xml.Element("MinDecoyScan") != null)
{
MinDecoyScan = int.Parse(xml.Element("MinDecoyScan").Value);
}
else
{
MinDecoyScan = MascotGenericFormatShiftPrecursorProcessorOptions.DEFAULT_ShiftScan;
}
if (xml.Element("MinTargetDecoySpectraRatio") != null)
{
MinTargetDecoySpectraRatio = double.Parse(xml.Element("MinTargetDecoySpectraRatio").Value);
}
else
{
MinTargetDecoySpectraRatio = 2.0;
}
}
public virtual void LoadFromFile(string fileName)
{
if (!File.Exists(fileName))
{
throw new FileNotFoundException("Parameter file not found", fileName);
}
XmlDocument doc = new XmlDocument();
doc.Load(fileName);
XmlNode docRoot = doc.DocumentElement;
var xmlHelper = new XmlHelper(doc);
this.ApplicationTitle = xmlHelper.GetChildValue(docRoot, "Version");
this.SearchEngine = xmlHelper.GetChildValue(docRoot, "SearchEngine");
XmlNode fdrXml = xmlHelper.GetValidChild(docRoot, "FalseDiscoveryRate");
if (null != fdrXml)
{
this.FilterByFdr = bool.Parse(xmlHelper.GetChildValue(fdrXml, "Filtered"));
this.FdrLevel = (FalseDiscoveryRateLevel)Enum.Parse(FalseDiscoveryRateLevel.Peptide.GetType(), xmlHelper.GetChildValue(fdrXml, "Level"), true);
this.FdrType = (FalseDiscoveryRateType)Enum.Parse(FalseDiscoveryRateType.Target.GetType(), xmlHelper.GetChildValue(fdrXml, "Type"), true);
this.FdrValue = MyConvert.ToDouble(xmlHelper.GetChildValue(fdrXml, "Value"));
this.MaxPeptideFdr = MyConvert.ToDouble(xmlHelper.GetChildValue(fdrXml, "MaxPeptideFdr", "0.01"));
if (xmlHelper.HasChild(fdrXml, "FdrPeptideCount"))
{
this.FdrPeptideCount = Convert.ToInt32(xmlHelper.GetChildValue(fdrXml, "FdrPeptideCount"));
}
this.FdrScoreType = xmlHelper.GetChildValue(fdrXml, "ScoreType");
this.ClassifyByCharge = bool.Parse(xmlHelper.GetChildValue(fdrXml, "ClassifyByCharge"));
this.ClassifyByMissCleavage = bool.Parse(xmlHelper.GetChildValue(fdrXml, "ClassifyByMissCleavage"));
this.ClassifyByModification = bool.Parse(xmlHelper.GetChildValue(fdrXml, "ClassifyByModification"));
this.ClassifyByNumProteaseTermini = bool.Parse(xmlHelper.GetChildValue(fdrXml, "ClassifyByNumProteaseTermini", true.ToString()));
this.ModifiedAminoacids = xmlHelper.GetChildValue(fdrXml, "ModifiedAminoacid");
this.ClassifyByProteinTag = bool.Parse(xmlHelper.GetChildValue(fdrXml, "ClassifyByProteinTag", false.ToString()));
this.ProteinTag = xmlHelper.GetChildValue(fdrXml, "ProteinTag", string.Empty);
this.TargetDecoyConflictType = ResolveTargetDecoyConflictTypeFactory.Find(xmlHelper.GetChildValue(fdrXml, "TargetDecoyConflictType", ResolveTargetDecoyConflictTypeFactory.Decoy.Name));
}
XmlNode peptideFilterXml = xmlHelper.GetValidChild(docRoot, "PeptideFilter");
if (null != peptideFilterXml)
{
LoadPeptideFilter(peptideFilterXml);
}
XmlNode databaseXml = xmlHelper.GetValidChild(docRoot, "Database");
this.Database.Location = xmlHelper.GetChildValue(databaseXml, "Location");
this.Database.AccessNumberPattern = xmlHelper.GetChildValue(databaseXml, "AccessNumberPattern").Replace(">", ">");
this.Database.DecoyPattern = xmlHelper.GetChildValue(databaseXml, "DecoyPattern").Replace(">", ">");
if (xmlHelper.HasChild(databaseXml, "ContaminationPattern"))
{
this.Database.ContaminationNamePattern = xmlHelper.GetChildValue(databaseXml, "ContaminationPattern").Replace(">", ">");
}
this.Database.RemovePeptideFromDecoyDB = bool.Parse(xmlHelper.GetChildValue(databaseXml, "RemovePeptideFromDecoyDB"));
LoadSpecialDefinition(docRoot);
XmlNode filesXml = xmlHelper.GetValidChild(docRoot, "PathNames");
if (null == filesXml)
{
throw new ArgumentException(MyConvert.Format("There is no PathNames section in parameter file {0}", fileName));
}
this.pathNameBin.Clear();
XmlNode pathNameXml = filesXml.FirstChild;
while (null != pathNameXml)
{
string bin = pathNameXml.Attributes["Bin"].Value;
this.pathNameBin[pathNameXml.InnerText] = bin;
pathNameXml = pathNameXml.NextSibling;
}
}