public void SetupMassAndNetAlignment(string alignmentFolder = "")
{
WorkflowExecutorBaseParameters massNetAlignerParameters = new BasicTargetedWorkflowExecutorParameters();
IqMassAndNetAligner = new IqMassAndNetAligner(massNetAlignerParameters, Run);
IqMassAndNetAligner.LoessBandwidthNetAlignment = 0.1;
//check if alignment info exists already
SetupAlignmentFolder(alignmentFolder);
var expectedAlignmentFilename = Path.Combine(_alignmentFolder, Run.DatasetName + "_iqAlignmentResults.txt");
var alignmentResultsExist = (File.Exists(expectedAlignmentFilename));
if (alignmentResultsExist)
{
IqLogger.Log.Info("Using the IQ alignment results from here: " + expectedAlignmentFilename);
IqMassAndNetAligner.LoadPreviousIqResults(expectedAlignmentFilename);
SetMassTagReferencesForNetAlignment();
return;
}
//Get a suitable targets file for alignment. These are grabbed from the ..\AlignmentInfo folder.
var targetFileForAlignment = GetTargetFilePathForIqAlignment();
if (string.IsNullOrEmpty(targetFileForAlignment))
{
IqLogger.Log.Info("Alignment not performed - No suitable target file found for use in alignment.");
return;
}
if (!File.Exists(targetFileForAlignment))
{
IqLogger.Log.Info("Alignment not performed - Target file for alignment has been specified but a FILE NOT FOUND error has occured.");
return;
}
var isFirstHitsFile = targetFileForAlignment.EndsWith("_fht.txt");
if (!isFirstHitsFile)
{
IqLogger.Log.Info("Alignment not performed - target file for alignment must be a first hits file (_fht.txt)");
return;
}
IqMassAndNetAligner.LoadAndInitializeTargets(targetFileForAlignment);
SetMassTagReferencesForNetAlignment();
}
public void AlignUsingPreviouslyProcessedOutputTest1()
{
var rawFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var previouslyProcessedResultsFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_iqAlignmentResults.txt";
WorkflowExecutorBaseParameters parameters = new BasicTargetedWorkflowExecutorParameters();
var run = new RunFactory().CreateRun(rawFile);
var massAndNetAligner = new IqMassAndNetAligner(parameters, run);
massAndNetAligner.LoadPreviousIqResults(previouslyProcessedResultsFile);
massAndNetAligner.ExecuteAlignment();
var baseFilenameForImageExport =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18";
massAndNetAligner.ExportGraphs(baseFilenameForImageExport);
}
