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();
}
/// <summary>
/// A factory method for creating the WorkflowParameters class. Based on the 'WorkflowType' parameter of the xml file.
/// </summary>
/// <param name="xmlFilepath"></param>
/// <returns></returns>
public static WorkflowParameters CreateParameters(string xmlFilepath)
{
Check.Require(File.Exists(xmlFilepath), "Workflow parameter file could not be loaded. File not found: " + xmlFilepath);
var doc = XDocument.Load(xmlFilepath);
var xElement = doc.Element("WorkflowParameters");
if (xElement == null)
{
throw new Exception("WorkflowParameters element not found in " + xmlFilepath);
}
var query = xElement.Elements();
var parameterTableFromXML = new Dictionary <string, string>();
foreach (var item in query)
{
var paramName = item.Name.ToString();
var paramValue = item.Value;
if (!parameterTableFromXML.ContainsKey(paramName))
{
parameterTableFromXML.Add(paramName, paramValue);
}
}
Globals.TargetedWorkflowTypes workflowType;
var successfulEnum = Enum.TryParse(parameterTableFromXML["WorkflowType"], out workflowType);
WorkflowParameters workflowParameters;
if (successfulEnum)
{
switch (workflowType)
{
case Globals.TargetedWorkflowTypes.Undefined:
workflowParameters = new BasicTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.UnlabelledTargeted1:
workflowParameters = new BasicTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.O16O18Targeted1:
workflowParameters = new O16O18WorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.N14N15Targeted1:
workflowParameters = new N14N15Workflow2Parameters();
break;
case Globals.TargetedWorkflowTypes.SipperTargeted1:
workflowParameters = new SipperTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.TargetedAlignerWorkflow1:
workflowParameters = new TargetedAlignerWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.BasicTargetedWorkflowExecutor1:
workflowParameters = new BasicTargetedWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.LcmsFeatureTargetedWorkflowExecutor1:
workflowParameters = new LcmsFeatureTargetedWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.SipperWorkflowExecutor1:
workflowParameters = new SipperWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.TopDownTargeted1:
workflowParameters = new TopDownTargetedWorkflowParameters();
break;
case Globals.TargetedWorkflowTypes.TopDownTargetedWorkflowExecutor1:
workflowParameters = new TopDownTargetedWorkflowExecutorParameters();
break;
case Globals.TargetedWorkflowTypes.UIMFTargetedMSMSWorkflowCollapseIMS:
workflowParameters = new UIMFTargetedMSMSWorkflowCollapseIMSParameters();
break;
default:
workflowParameters = new BasicTargetedWorkflowParameters();
break;
}
}
else
{
throw new ArgumentOutOfRangeException(
"Tried to create WorkflowParameter object. But WorkflowType is unknown.");
}
workflowParameters.LoadParameters(xmlFilepath);
return(workflowParameters);
}