protected override IqResult CreateIqResult()
{
IqTarget target = new IqChargeStateTarget();
var result = new IqResult(target);
return(result);
}
public void Test1()
{
TargetedWorkflowParameters o16o18workflowParameters = new O16O18WorkflowParameters();
var parentWorkflow = new O16O18IqWorkflow(o16o18workflowParameters);
TargetedWorkflowParameters workflowParameters = new BasicTargetedWorkflowParameters();
var childWorkflow = new BasicIqWorkflow(workflowParameters);
IqTarget parentTarget = new IqChargeStateTarget();
IqTarget childTarget1 = new IqChargeStateTarget();
IqTarget childTarget2 = new IqChargeStateTarget();
IqTarget childTarget3 = new IqChargeStateTarget();
parentTarget.AddTarget(childTarget1);
parentTarget.AddTarget(childTarget2);
parentTarget.AddTarget(childTarget3);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, parentTarget);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, parentTarget);
Assert.IsNotNull(parentTarget.ChildTargets().First().Workflow);
var childTargets = parentTarget.ChildTargets();
foreach (var childTarget in childTargets)
{
Assert.IsTrue(childTarget.Workflow is BasicIqWorkflow);
}
Assert.IsTrue(parentTarget.Workflow is O16O18IqWorkflow);
}
public void FailureToFindAnyChromatogramDataTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromGenTolerance = 1; //very narrow tolerance
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.EmpiricalFormula = DeconTools.Backend.Utilities.IsotopeDistributionCalculation.IsotopicDistributionCalculator.Instance.GetAveragineFormulaAsString(1399);
target.ElutionTimeTheor = 0.3;
target.ChargeState = 1;
target.DoWorkflow();
var result = target.GetResult();
Assert.IsTrue(result.Target.TheorIsotopicProfile != null);
Assert.IsTrue(result != null);
Assert.IsTrue(result.IqResultDetail.Chromatogram == null);
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
protected override IqTarget ConvertTextToIqTarget(List <string> processedRowOfText)
{
var child = new IqChargeStateTarget();
child.ChargeState = ParseIntField(processedRowOfText, ChargeHeader);
child.ObservedScan = ParseIntField(processedRowOfText, ScansHeader);
child.AlternateID = ParseIntField(processedRowOfText, PRSMIdHeader);
child.DatabaseReference = ParseStringField(processedRowOfText, ProteinNameHeader);
return(child);
}
public void ChromCorrelatorTest1()
{
var rawFilename = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
var run = new RunFactory().CreateRun(rawFilename);
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new IqExecutor(executorBaseParameters, run);
executor.LoadChromData(run);
var workflowAssigner = new IqWorkflowAssigner();
TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters();
IqWorkflow workflow = new O16O18IqWorkflow(run, workflowParameters);
IqTarget iqTarget = new IqChargeStateTarget();
iqTarget.EmpiricalFormula = "C58H100N18O20";
iqTarget.Code = "GAAQNIIPASTGAAK";
iqTarget.ID = 1093;
iqTarget.ChargeState = 0;
var iqTargetList = new List <IqTarget>();
iqTargetList.Add(iqTarget);
var utilities = new IqTargetUtilities();
utilities.CreateChildTargets(iqTargetList);
workflowAssigner.AssignWorkflowToParent(workflow, iqTargetList);
workflowAssigner.AssignWorkflowToChildren(workflow, iqTargetList);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
foreach (var target in iqTarget.ChildTargets())
{
utilities.UpdateTargetMissingInfo(target);
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
}
foreach (var childTarget in iqTarget.ChildTargets())
{
var result = childTarget.CreateResult();
var correlator = new O16O18ChromCorrelator(7, 0.1, 20, Globals.ToleranceUnit.PPM);
var corrData = correlator.CorrelateData(run, result, 5700, 6500);
var corrDataItem1 = corrData.CorrelationDataItems.First();
Console.WriteLine("z= \t" + childTarget.ChargeState + "\tCorrelationData (slope,intercept,rsquared)= \t" + corrDataItem1);
}
}
public void NodeLevelTest1()
{
var util = new IqTargetUtilities();
IqTarget iqTarget1 = new IqChargeStateTarget();
IqTarget iqTarget2 = new IqChargeStateTarget();
IqTarget iqTarget3_1 = new IqChargeStateTarget();
iqTarget3_1.ID = 3001;
IqTarget iqTarget3_2 = new IqChargeStateTarget();
iqTarget3_2.ID = 3002;
IqTarget iqTarget4 = new IqChargeStateTarget();
IqTarget iqTarget5 = new IqChargeStateTarget();
iqTarget4.AddTarget(iqTarget5);
iqTarget3_1.AddTarget(iqTarget4);
iqTarget2.AddTarget(iqTarget3_1);
iqTarget2.AddTarget(iqTarget3_2);
iqTarget1.AddTarget(iqTarget2);
var rootNode = iqTarget5.RootTarget;
Assert.AreEqual(rootNode, iqTarget1);
var nodeLevelCount = util.GetTotalNodelLevels(iqTarget1);
Assert.AreEqual(5, nodeLevelCount);
nodeLevelCount = util.GetTotalNodelLevels(iqTarget5);
Assert.AreEqual(5, nodeLevelCount);
var targetList = new List <IqTarget>();
targetList.Add(iqTarget1);
var level2Targets = util.GetTargetsFromNodelLevel(targetList, 2);
foreach (var level2Target in level2Targets)
{
Console.WriteLine(level2Target);
}
}
public void ChromPeakAnalyzerWorkflowWrongTargetTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
IqTarget testTarget = new IqChargeStateTarget();
testTarget.SetWorkflow(new ChromPeakAnalyzerIqWorkflow(run, parameters));
testTarget.DoWorkflow();
}
public void IqWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-709
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
var oldStyleTarget = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.ID = oldStyleTarget.ID;
target.MZTheor = oldStyleTarget.MZ;
target.ElutionTimeTheor = oldStyleTarget.NormalizedElutionTime;
target.MonoMassTheor = oldStyleTarget.MonoIsotopicMass;
target.EmpiricalFormula = oldStyleTarget.EmpiricalFormula;
target.ChargeState = oldStyleTarget.ChargeState;
Console.WriteLine(target.EmpiricalFormula + "\t" + target.ChargeState);
target.DoWorkflow();
var result = target.GetResult();
Assert.IsNotNull(result, "result is null");
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var testPeak = new ChromPeak(5184, 840963, 50, 0);
var executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
var workflow = new ChromPeakAnalyzerIqWorkflow(run, parameters);
testTarget.SetWorkflow(workflow);
testTarget.ID = 1;
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
var testTargetList = new List <IqTarget>();
IqTarget testParent = new IqChargeStateTarget();
testParent.AddTarget(testTarget);
testTargetList.Add(testTarget);
executor.Execute(testTargetList);
var result = testTarget.GetResult();
Assert.NotNull(result.LCScanSetSelected);
Assert.AreNotEqual(1, result.FitScore);
Assert.AreEqual(true, result.IsotopicProfileFound);
}
protected override IqTarget ConvertTextToIqTarget(List <string> processedRow)
{
IqTarget target = new IqChargeStateTarget();
target.ID = ParseIntField(processedRow, TargetIDHeaders, -1);
if (target.ID == -1)
{
target.ID = GetAutoIncrementForTargetID();
}
target.EmpiricalFormula = ParseStringField(processedRow, EmpiricalFormulaHeaders, string.Empty);
target.Code = ParseStringField(processedRow, CodeHeaders, "");
target.ElutionTimeTheor = ParseDoubleField(processedRow, NETHeaders, 0);
target.ScanLC = ParseIntField(processedRow, ScanHeaders, -1);
target.QualityScore = ParseDoubleField(processedRow, QualityScoreHeaders, -1);
target.ChargeState = ParseIntField(processedRow, ChargeStateHeaders, 0);
return(target);
}
public static IqTarget GetIQTargetStandard(int standardNum)
{
//MassTagID MonoisotopicMass NET NETStDev Obs minMSGF mod_count mod_description pmt_quality_score peptide peptideex Multiple_Proteins
//86963986 1516.791851 0.227147 0.007416702 3 1 0 2.00000 AAKEGISCEIIDLR M.AAKEGISCEIIDLR.T 0
IqTarget target = new IqChargeStateTarget(null);
target.ID = 86963986;
target.MonoMassTheor = 1516.791851;
target.EmpiricalFormula = "C64H112N18O22S";
target.Code = "AAKEGISCEIIDLR";
target.ChargeState = 2;
target.ElutionTimeTheor = 0.227147;
target.MZTheor = target.MonoMassTheor / target.ChargeState + Globals.PROTON_MASS;
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
return(target);
}
public void IqExportResultsTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-832
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
var oldStyleTarget = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.ID = oldStyleTarget.ID;
target.MZTheor = oldStyleTarget.MZ;
target.ElutionTimeTheor = oldStyleTarget.NormalizedElutionTime;
target.MonoMassTheor = oldStyleTarget.MonoIsotopicMass;
target.EmpiricalFormula = oldStyleTarget.EmpiricalFormula;
target.ChargeState = oldStyleTarget.ChargeState;
var targets = new List <IqTarget>(1);
targets.Add(target);
var executor = new IqExecutor(executorBaseParameters, run);
//executor.ChromSourceDataFilePath = peaksTestFile;
executor.Execute(targets);
Assert.IsTrue(File.Exists(@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_iqResults.txt"));
using (var reader = new StreamReader(@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_iqResults.txt"))
{
var temp = reader.ReadLine();
Assert.AreEqual(
"TargetID\tCode\tEmpiricalFormula\tChargeState\tMonomassTheor\tMZTheor\tElutionTimeTheor\tMonoMassObs\tMZObs\tElutionTimeObs\tChromPeaksWithinTolerance\tScan\tAbundance\tIsoFitScore\tInterferenceScore",
temp);
temp = reader.ReadLine();
Console.WriteLine(temp);
Assert.AreEqual(
"24800\t\tC64H110N18O19\t2\t1434.8193888\t718.41697089\t0.321639209985733\t1434.81096195126\t718.412757465632\t0.318046778440475\t0\t5942\t1352176\t0.0850492709063084\t0.0942918054560866",
temp);
}
}