public DocumentAnalyzerController(IDocumentAnalyzerService documentAnalyzerService, IMlModelService mlModelService, IResultAnalyzer resultAnalyzer, ILogger <DocumentAnalyzerController> logger)
{
_documentAnalyzerService = documentAnalyzerService;
_mlModelService = mlModelService;
_resultAnalyzer = resultAnalyzer;
_logger = logger;
}
public virtual void Read(string peptideFileLocation, string spectrumFileLocation)
{
List <IPeptide> peptides = initializer.GetPeptides(peptideFileLocation);
spectrumRunner = initializer.GetSpectrumReader(spectrumFileLocation);
int lastScan = spectrumRunner.GetLastScan();
resultTable = new IGlycoPeptideScoreResultProduct[lastScan + 1];
glycanGenerator = new BruteForceNGlycanCreator(initializer.GetGlycanCreatorParameter());
glycans = glycanGenerator.Generate();
// data process
specProcessor = initializer.GetSpectrumProcessing();
monoRunner = new BinSearchMonoMassSpectrumRun();
// precursor
double preTol = initializer.GetParameter().GetMS1Tolereance();
precursorMatcher = new Y1PeptidesFilterPrecursorMatcher(
new GlycoPeptidePrecursorMatcher(peptides, glycans, preTol), peptides);
// search spectrum
double tol = initializer.GetParameter().GetMSMSTolereance();
searchWorker = new DPSearchSpectrumCID(tol);
//result
analyzer = new GeneralGlycoPeptideScoreResultAnalyzer();
}
public PrintTestRunner(string name, IResultGenerator resultGenerator, IResultAnalyzer resultAnalyzer)
{
this.resultGenerator = resultGenerator;
this.resultAnalyzer = resultAnalyzer;
directory = TestDataPaths.GetTestDataDirectory(name);
}
public void AnalyzeRange(int start, int end)
{
discover.Compute();
analyzer = new ScoreCutoffGlycoPeptideScoreResultAnalyzer(discover.GetCutoffScore());
//analyzer = new GeneralGlycoPeptideScoreResultAnalyzer();
analyzer.Init(initializer.GetOutputLocation());
for (int i = start; i <= end; i++)
{
Analyze(i);
}
analyzer.Exit();
}