public ViewAndAnnotateViewModel()
{
FileInputs = new FileInputsViewModel();
_resultRepositorySource = new TargetedResultRepository();
Results = new ObservableCollection<SipperLcmsFeatureTargetedResultDTO>();
var workflowParameters = new SipperTargetedWorkflowParameters();
Workflow = new SipperTargetedWorkflow(workflowParameters);
ChromGraphXWindowWidth = 600;
MsGraphMinX = 400;
MsGraphMaxX = 1400;
ShowFileAndResultsList = true;
MassSpecVisibleWindowWidth = 15;
}
public ResultImageOutputter(FileInputsInfo fileInputs, BackgroundWorker worker = null)
{
_fileInputs = fileInputs;
_backgroundWorker = worker;
WorkflowParameters = new SipperTargetedWorkflowParameters();
Workflow = new SipperTargetedWorkflow(WorkflowParameters);
ChromGraphXWindowWidth = 400;
NumResultsPerFolder = 200;
InitializeGraphs();
}
public void executeWorkflowTest1()
{
var testFile = FileRefs.SipperRawDataFile;
var peaksFile =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2012\C12C13YellowStone\2011_02_20_SIPPER_workflow_standards\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
peaksFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksFile);
var lcmsfeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
var masstagIDlist = (from n in massTagCollection.TargetList select n.ID).ToList();
// Update LCMSFeatures using MassTag info
int[] testMassTags = { 344540889, 344972415, 354881152, 355157363, 355162540, 355315129, 355054192, 355160150 };
//testMassTags = new[] {344540889};
//testMassTags = new int[]
// {
// 354942933, 355066611, 354882356, 354928525, 17440471, 355046165, 355008036, 354977066,
// 355166304, 354879605, 344965520, 354870998, 355084057, 355034961, 354963652, 344969970,
// 355157492, 355176429, 355162540, 355244316, 355139611, 355036935, 355044786, 355139579,
// 355163558, 355065622, 355167968, 355033793, 354879421, 355090391, 355034165, 354880925,
// 344747857, 354879494, 355315129, 344968376, 355022502, 354879347, 354881152, 354879406,
// 344968302, 355037491, 355033717, 355034652, 354879414, 344972415, 355039789, 355025762,
// 355129038, 355355053, 354879164, 355037247, 355033862, 355034180, 355033668, 344540889,
// 355160123, 345073233, 354880183, 354879165, 354879192, 354879842, 355046211, 355033627,
// 355030074, 355033620, 354879142, 354879360, 355034183, 354879174, 354879150
// };
//no enrichment peptides:
//testMassTags = new int[] { 355057553, 355058671, 355084418 };
//enriched
//testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };
//testMassTags = new int[] { 355008295 };
//co-elution peptides
//testMassTags = new int[] {355034154, 355033668, 355154211, 355035781};
//testMassTags = new int[] { 355033668 };
//testMassTags = new int[]{355157492};
testMassTags = new int[] { 355033977 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
foreach (LcmsFeatureTarget target in filteredLcmsFeatureTargets)
{
if (masstagIDlist.Contains(target.FeatureToMassTagID))
{
var mt = massTagCollection.TargetList.Where(p => p.ID == target.FeatureToMassTagID).First();
target.Code = mt.Code;
target.EmpiricalFormula = mt.EmpiricalFormula;
}
else
{
//get target's code + empirical formula based on averagine model
}
}
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var workflow = new SipperTargetedWorkflow(run, parameters);
var outputFolder = @"C:\data\temp\SipperOutput";
if (!Directory.Exists(outputFolder))
{
Directory.CreateDirectory(outputFolder);
}
var stopwatch = new Stopwatch();
stopwatch.Start();
foreach (var target in filteredLcmsFeatureTargets)
{
run.CurrentMassTag = target;
workflow.Execute();
OutputMassSpectrum(outputFolder, workflow.MassSpectrumXYData, target, workflow.Result as SipperLcmsTargetedResult);
}
stopwatch.Stop();
foreach (var targetedResultBase in (run.ResultCollection.MassTagResultList))
{
var result = (SipperLcmsTargetedResult)targetedResultBase.Value;
Console.WriteLine(result + "\t" + result.Target.IsotopicProfile.Peaklist.Count);
}
Console.WriteLine("Total workflow time (ms) = " + stopwatch.ElapsedMilliseconds);
Console.WriteLine("Time per target (ms) = " + stopwatch.ElapsedMilliseconds / (double)filteredLcmsFeatureTargets.Count);
}
public void executeWorkflowTest1()
{
var testFile = FileRefs.SipperRawDataFile;
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "ExportedSipperResults1.txt");
var peaksFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksFile);
var lcmsfeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
//enriched
var testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
TargetCollection.UpdateTargetsWithMassTagInfo(filteredLcmsFeatureTargets, massTagCollection.TargetList);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var workflow = new SipperTargetedWorkflow(run, parameters);
foreach (var target in filteredLcmsFeatureTargets)
{
run.CurrentMassTag = target;
workflow.Execute();
}
var results = run.ResultCollection.GetMassTagResults();
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new SipperResultToLcmsFeatureExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}