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 UniformSummaryBuilderUI()
{
InitializeComponent();
Option = new BuildSummaryOptions();
InsertButton(2, btnNew);
InsertButton(3, this.btnLoadParam);
InsertButton(4, this.btnSaveParam);
this.minDecoyScan.DefaultValue = MascotGenericFormatShiftPrecursorProcessorOptions.DEFAULT_ShiftScan.ToString();
this.decoyPattern = new RcpaTextField(this.txtDecoyPattern, "DecoyPattern", "Decoy Database Pattern", "^REVERSED_", false);
AddComponent(this.decoyPattern);
this.removeContamination = new RcpaCheckBox(cbRemoveContamination, "RemoveContamination", false);
AddComponent(this.removeContamination);
this.contaminationNamePattern = new RcpaTextField(this.txtContaminantString, "ContaminationNamePattern", "Contaminant Name Pattern", "CON_", false);
AddComponent(this.contaminationNamePattern);
this.contaminationDescriptionPattern = new RcpaTextField(this.txtContaminantDescriptionPattern, "ContaminantDescriptionPattern", "Contaminant Description Pattern", "KERATIN", false);
AddComponent(this.contaminationDescriptionPattern);
this.filterByFdr = new RcpaCheckBox(this.cbFilterByFDR, "FilterByFDR", true);
AddComponent(this.filterByFdr);
this.maxFdr = new RcpaDoubleField(this.txtMaxFdr, "MaxFdr", "Max False Discovery Rate", 0.01, true);
AddComponent(this.maxFdr);
this.maxPeptideFdr = new RcpaDoubleField(this.txtMaxPeptideFdr, "MaxPeptideFdr", "Max Peptide FDR", 0.01, true);
AddComponent(this.maxPeptideFdr);
this.filterProteinByPeptideCount = new RcpaCheckBox(this.cbPeptideCount, "FilterProteinByPeptideCount", false);
AddComponent(this.filterProteinByPeptideCount);
this.fdrLevel = new RcpaComboBox <FalseDiscoveryRateLevel>(this.cbFdrLevel, "FdrLevel",
new[]
{
FalseDiscoveryRateLevel.Peptide,
FalseDiscoveryRateLevel.Protein,
FalseDiscoveryRateLevel.SimpleProtein,
FalseDiscoveryRateLevel.UniquePeptide
}, 1);
AddComponent(this.fdrLevel);
this.peptideRetrieval = new RcpaCheckBox(this.cbPeptideRetrieval, "PeptideRetrieval", true);
AddComponent(this.peptideRetrieval);
this.fdrType = new RcpaComboBox <FalseDiscoveryRateType>(this.cbFdrType, "FdrType",
new[]
{
FalseDiscoveryRateType.Target,
FalseDiscoveryRateType.Total
},
new[]
{
"Target : N(decoy) / N(target)",
"Global : N(decoy) * 2 / (N(decoy) + N(target))"
}, 0);
AddComponent(this.fdrType);
this.classifyByCharge = new RcpaCheckBox(this.cbClassifyByCharge, "ClassifyByCharge", ClassificationOptions.DEFAULT_ClassifyByCharge);
AddComponent(this.classifyByCharge);
this.classifyByMissCleavage = new RcpaCheckBox(this.cbClassifyByMissCleavage, "ClassifyByMissCleavage", ClassificationOptions.DEFAULT_ClassifyByMissCleavage);
AddComponent(this.classifyByMissCleavage);
this.classifyByNumberOfProteaseTermini = new RcpaCheckBox(this.cbClassifyByPreteaseTermini, "ClassifyByNumberOfProteaseTermini", ClassificationOptions.DEFAULT_ClassifyByNumProteaseTermini);
AddComponent(this.classifyByNumberOfProteaseTermini);
this.classifyByModification = new RcpaCheckBox(this.cbClassifyByModification, "ClassifyByModification", ClassificationOptions.DEFAULT_ClassifyByModification);
AddComponent(this.classifyByModification);
this.modifiedAminoacids = new RcpaTextField(this.txtFdrModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", true);
this.modifiedAminoacids.PreCondition = this.cbClassifyByModification;
AddComponent(this.modifiedAminoacids);
this.classifyByProteinTag = new RcpaCheckBox(this.cbClassifyByProteinTag, "ClassifyByProteinTag", ClassificationOptions.DEFAULT_ClassifyByProteinTag);
AddComponent(this.classifyByProteinTag);
this.proteinTag = new RcpaTextField(this.txtProteinTag, "ProteinTag", "Protein Tag", "", false);
this.proteinTag.PreCondition = this.cbClassifyByProteinTag;
AddComponent(this.proteinTag);
this.minimumSpectraPerGroup = new RcpaIntegerField(this.txtMinimumSpectraPerGroup, "MinimumSpectraPerGroup", "MinimumSpectraPerGroup", ClassificationOptions.DEFAULT_MinimumSpectraPerGroup, true);
AddComponent(this.minimumSpectraPerGroup);
this.filterSequenceLength = new RcpaCheckBox(this.cbSequenceLength, "FilterSequenceLength", false);
AddComponent(this.filterSequenceLength);
this.minSequenceLength = new RcpaIntegerField(this.txtMinSequenceLength, "MinSequenceLength", "Minmum Sequence Length", PeptideFilterOptions.DEFAULT_MinSequenceLength, false);
this.minSequenceLength.PreCondition = cbSequenceLength;
AddComponent(this.minSequenceLength);
this.filterMaxMissCleavage = new RcpaCheckBox(this.cbMaxMissCleavage, "FilterMaxMisscleavage", false);
AddComponent(this.filterMaxMissCleavage);
this.maxMissCleagage = new RcpaIntegerField(this.txtMaxMissCleavage, "MaxMissCleavage", "Maximum Number of Internal Missed Cleavage", PeptideFilterOptions.DEFAULT_MaxMissCleavage, false);
this.maxMissCleagage.PreCondition = cbMaxMissCleavage;
AddComponent(this.maxMissCleagage);
this.removeDecoyEntry = new RcpaCheckBox(this.cbRemoveDecoyEntry, "RemovePeptideFromDecoyDB", false);
AddComponent(this.removeDecoyEntry);
this.database = new RcpaFileField(btnDatabase, txtDatabase, "Database", new OpenFileArgument("Protein Database", "fasta"), "", true);
AddComponent(this.database);
this.acParsers = new RcpaComboBox <IAccessNumberParser>(this.cbAccessNumberPattern, "AccessNumberPattern", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(this.acParsers);
this.seConflictType = new RcpaComboBox <IResolveSearchEngineConflictType>(cbConflict, "ConflictType", ResolveSearchEngineConflictTypeFactory.GetTypes(), 1);
AddComponent(this.seConflictType);
this.conflictAsDecoy = new RcpaComboBox <ITargetDecoyConflictType>(cbConflictAsDecoy, "ConflictAsDecoy", ResolveTargetDecoyConflictTypeFactory.GetTypes(), 0);
AddComponent(this.conflictAsDecoy);
this.minAgreeCount = new RcpaIntegerField(txtMinAgreeCount, "MinAgreeCount", "Minimum agree count of engines", 1, true);
AddComponent(this.minAgreeCount);
minOneHitWonderPeptideCount = new RcpaIntegerField(txtMinOneHitWonderPeptideCount, "MinOneHitWonderPeptideCount", "minimum one-hit-wonder peptide count", 2, false);
AddComponent(minOneHitWonderPeptideCount);
minOneHitWonderPeptideCount.PreCondition = FilterOneHitWonder;
this.AfterLoadOption += DoAfterLoadOption;
Text = Constants.GetSQHTitle(title, version);
var engines = EnumUtils.EnumToArray <SearchEngineType>().OrderByDescending(m => m.ToString()).ToArray();
foreach (var engine in engines)
{
if (engine.HasFactory())
{
var button = new Button();
pnlAdd.Controls.Add(button);
button.Dock = System.Windows.Forms.DockStyle.Top;
button.UseVisualStyleBackColor = true;
button.Text = "Add " + engine.ToString();
button.Name = "btnAdd" + engine.ToString();
button.Tag = engine;
button.Click += button_Click;
}
}
pnlAdd.Update();
}
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;
}
}
