public void TestClassifyWithModelPipeline()
{
AnalysisPipeline pipeline = new AnalysisPipeline(MS1MatchFile, GlycosylationSitesFile, MS2DeconvolutionFile, ModelJsonFile, null, 1e-5, 2e-5, proteinProspectorXMLFilePath: ProteinProspectorXmlFile);
ResultsRepresentation result = pipeline.RunClassification();
Assert.IsInstanceOfType(result, typeof(ResultsRepresentation));
}
static ResultsRepresentation TestFullRun()
{
Console.WriteLine("TestFullRun");
AnalysisPipeline pipeline = new AnalysisPipeline(Properties.Resources.TestMS1Matches,
Properties.Resources.TestGlycosylationSites, Properties.Resources.TestDeconvolutedMS2,
Properties.Resources.TestGoldStandard,
ms1MatchingTolerance:1e-5,
ms2MatchingTolerance:2e-5,
constantModifications: Modifications,
variableModifications: Modifications,
method:"default",
outputFilePath:"test.csv",
rscriptPath: Properties.Resources.DevelRscriptPath);
ResultsRepresentation results = null;
try
{
results = pipeline.RunClassification();
}
catch (Exception e)
{
Console.WriteLine(e.Message);
throw;
}
int i = 0;
foreach (GlycopeptidePrediction pred in results.MatchedPredictions)
{
Console.WriteLine(pred);
i++;
if (i > 5) break;
}
Console.WriteLine(pipeline.Scripter.LastCall.Out);
return results;
}
/// <summary>
/// Runs the Model Building Pipeline, yielding a partially annotated model in the form of a ResultsRepresentation object
/// which is made from the parameters loaded into the Controller.
/// </summary>
/// <returns></returns>
public ResultsRepresentation PrepareModelFile()
{
this.Pipeline = new AnalysisPipeline(MS1MatchFilePath,
GlycosylationSiteFilePath, MS2DeconvolutionFilePath,
modelFilePath: ModelFilePath, outputFilePath: null,
proteinProspectorXMLFilePath: ProteinProspectorMSDigestFilePath,
ms1MatchingTolerance: ConfigurationManager.Algorithm.MS1MassErrorTolerance,
ms2MatchingTolerance: ConfigurationManager.Algorithm.MS2MassErrorTolerance,
numProcesses: ConfigurationManager.Algorithm.NumProcesses,
numDecoys: ConfigurationManager.Algorithm.NumDecoys,
onlyRandomDecoys: ConfigurationManager.Algorithm.OnlyRandomDecoys,
pythonInterpreterPath: ConfigurationManager.Scripting.PythonInterpreterPath,
rscriptPath: null);
ResultsRepresentation modelRepresentation = Pipeline.RunModelBuilder();
File.Delete(modelRepresentation.SourceFile);
return modelRepresentation;
}
public ResultsRepresentation ReclassifyWithModel(String reclassificationTargetFilePath)
{
this.Pipeline = new AnalysisPipeline(MS1MatchFilePath,
GlycosylationSiteFilePath, MS2DeconvolutionFilePath,
modelFilePath: ModelFilePath, outputFilePath: null,
ms1MatchingTolerance: ConfigurationManager.Algorithm.MS1MassErrorTolerance,
ms2MatchingTolerance: ConfigurationManager.Algorithm.MS2MassErrorTolerance,
pythonInterpreterPath: ConfigurationManager.Scripting.PythonInterpreterPath,
numProcesses: ConfigurationManager.Algorithm.NumProcesses,
numDecoys: ConfigurationManager.Algorithm.NumDecoys,
onlyRandomDecoys: ConfigurationManager.Algorithm.OnlyRandomDecoys,
rscriptPath: null);
ResultsRepresentation modelRepresentation = this.Pipeline.RunReclassification(reclassificationTargetFilePath, ModelFilePath);
File.Delete(modelRepresentation.SourceFile);
return modelRepresentation;
}
public ResultsRepresentation ClassifyGlycopeptideTandemMS()
{
try
{
this.Pipeline = new AnalysisPipeline(MS1MatchFilePath,
GlycosylationSiteFilePath, MS2DeconvolutionFilePath,
modelFilePath: ModelFilePath, outputFilePath: null,
proteinProspectorXMLFilePath: ProteinProspectorMSDigestFilePath,
ms1MatchingTolerance: ConfigurationManager.Algorithm.MS1MassErrorTolerance,
ms2MatchingTolerance: ConfigurationManager.Algorithm.MS2MassErrorTolerance,
numProcesses: ConfigurationManager.Algorithm.NumProcesses,
numDecoys: ConfigurationManager.Algorithm.NumDecoys,
onlyRandomDecoys: ConfigurationManager.Algorithm.OnlyRandomDecoys,
pythonInterpreterPath: ConfigurationManager.Scripting.PythonInterpreterPath,
rscriptPath: null);
ResultsRepresentation results = Pipeline.RunClassification();
File.Delete(results.SourceFile);
return results;
}
catch (TandemGlycoPeptidePipelineException e)
{
Console.WriteLine(e.Message);
MessageBox.Show("An error occurred during classification: " + e.Message, "Error");
throw;
}
}