public new void InitializeWorkflow()
{
_resultsFolder = string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase) ? RunUtilities.GetDatasetParentFolder(DatasetPath) : GetResultsFolder(ExecutorParameters.OutputFolderBase);
MassTagsForTargetedAlignment = GetMassTagTargets(GetTargetFilePathForIqAlignment());
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
var currentTargetsFilePath = targetsFilePathIsEmpty ? TryFindTargetsForCurrentDataset() : ExecutorParameters.TargetsFilePath;
Targets = CreateTargets(ExecutorParameters.TargetType, currentTargetsFilePath);
if (ExecutorParameters.TargetType == Globals.TargetType.LcmsFeature)
{
UpdateTargetMissingInfo();
}
if (_workflowParameters == null)
{
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetedAlignmentWorkflowParameterFile))
{
throw new FileNotFoundException(
"Cannot initialize workflow. TargetedAlignment is requested but TargetedAlignmentWorkflowParameter file is not found. Check path for the 'TargetedAlignmentWorkflowParameterFile' ");
}
TargetedAlignmentWorkflowParameters = new TargetedAlignerWorkflowParameters();
TargetedAlignmentWorkflowParameters.LoadParameters(ExecutorParameters.TargetedAlignmentWorkflowParameterFile);
}
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
public void InitializeWorkflow()
{
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
_resultsFolder = RunUtilities.GetDatasetParentFolder(DatasetPath);
}
else
{
_resultsFolder = GetResultsFolder(ExecutorParameters.OutputFolderBase);
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
MassTagsForTargetedAlignment = GetMassTagTargets(GetTargetFilePathForIqAlignment());
}
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
string currentTargetsFilePath;
if (targetsFilePathIsEmpty)
{
currentTargetsFilePath = TryFindTargetsForCurrentDataset(); //check for a _targets file specifically associated with dataset
}
else
{
currentTargetsFilePath = ExecutorParameters.TargetsFilePath;
}
Targets = CreateTargets(ExecutorParameters.TargetType, currentTargetsFilePath);
Check.Ensure(Targets != null && Targets.TargetList.Count > 0,
"Target massTags is empty (or all peptides contain unknown modifications). Check the path to the massTag data file.");
IqLogger.Log.Info("Total targets loaded= " + Targets.TargetList.Count);
if (ExecutorParameters.TargetType == Globals.TargetType.LcmsFeature)
{
UpdateTargetMissingInfo();
}
if (TargetedWorkflow == null)
{
if (_workflowParameters == null)
{
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
}
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
else
{
_workflowParameters = TargetedWorkflow.WorkflowParameters;
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetedAlignmentWorkflowParameterFile))
{
throw new FileNotFoundException(
"Cannot initialize workflow. TargetedAlignment is requested but TargetedAlignmentWorkflowParameter file is not found. Check path for the 'TargetedAlignmentWorkflowParameterFile' ");
}
TargetedAlignmentWorkflowParameters = new TargetedAlignerWorkflowParameters();
TargetedAlignmentWorkflowParameters.LoadParameters(ExecutorParameters.TargetedAlignmentWorkflowParameterFile);
}
}