Merge pull request #244 from smith-chem-wisc/StefanBranch

Stuffs

Author: stefanks

GUI/MainWindow.xaml.cs

@@ -503,9 +503,9 @@ private void ClearOutput_Click(object sender, RoutedEventArgs e)
         private void ResetTasksButton_Click(object sender, RoutedEventArgs e)
         {
             tasksGroupBox.IsEnabled = true;
-            ClearTasksButton.IsEnabled = false;
-            RemoveLastTaskButton.IsEnabled = false;
-            RunTasksButton.IsEnabled = false;
+            ClearTasksButton.IsEnabled = true;
+            RemoveLastTaskButton.IsEnabled = true;
+            RunTasksButton.IsEnabled = true;
             addCalibrateTaskButton.IsEnabled = true;
             addGPTMDTaskButton.IsEnabled = true;
             addSearchTaskButton.IsEnabled = true;

TaskLayer/CalibrationTask/CalibrationTask.cs

@@ -171,17 +171,18 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
                 IMsDataFile<IMsDataScan<IMzSpectrum<IMzPeak>>> myMsDataFile;
                 lock (lock1) // Lock because reading is sequential
                 {
-                    StartingDataFile(origDataFileName, new List<string> { taskId });
-                    Status("Loading spectra file " + origDataFileName + "...", new List<string> { taskId });
+                    NewCollection(Path.GetFileName(origDataFileName), new List<string> { taskId, "Individual Searches", origDataFileName });
+                    StartingDataFile(origDataFileName, new List<string> { taskId, "Individual Searches", origDataFileName });
+                    Status("Loading spectra file " + origDataFileName + "...", new List<string> { taskId, "Individual Searches", origDataFileName });
                     if (Path.GetExtension(origDataFileName).Equals(".mzML"))
                         myMsDataFile = Mzml.LoadAllStaticData(origDataFileName);
                     else
                         myMsDataFile = ThermoStaticData.LoadAllStaticData(origDataFileName);
-                    Status("Opening spectra file " + origDataFileName + "...", new List<string> { taskId });
+                    Status("Opening spectra file " + origDataFileName + "...", new List<string> { taskId, "Individual Searches", origDataFileName });
                     listOfSortedms2Scans = MyEngine.GetMs2Scans(myMsDataFile).OrderBy(b => b.MonoisotopicPrecursorMass).ToArray();
                 }
 
-                var searchEngine = new ClassicSearchEngine(listOfSortedms2Scans, myMsDataFile.NumSpectra, variableModifications, fixedModifications, proteinList, ProductMassTolerance, Protease, searchModes, MaxMissedCleavages, MaxModificationIsoforms, origDataFileName, lp, new List<string> { taskId });
+                var searchEngine = new ClassicSearchEngine(listOfSortedms2Scans, myMsDataFile.NumSpectra, variableModifications, fixedModifications, proteinList, ProductMassTolerance, Protease, searchModes, MaxMissedCleavages, MaxModificationIsoforms, origDataFileName, lp, new List<string> { taskId, "Individual Searches", origDataFileName });
 
                 var searchResults = (ClassicSearchResults)searchEngine.Run();
                 myTaskResults.AddResultText(searchResults);
@@ -191,7 +192,7 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
 
                 InitiatorMethionineBehavior initiatorMethionineBehavior = InitiatorMethionineBehavior.Variable;
                 // Run analysis on single file results
-                var analysisEngine = new AnalysisEngine(searchResults.OuterPsms, compactPeptideToProteinPeptideMatching, proteinList, variableModifications, fixedModifications, localizeableModifications, Protease, searchModes, myMsDataFile, ProductMassTolerance, (BinTreeStructure myTreeStructure, string s) => WriteTree(myTreeStructure, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, origDataFileName }), (List<NewPsmWithFdr> h, string s) => WritePsmsToTsv(h, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, origDataFileName }), null, false, false, MaxMissedCleavages, MaxModificationIsoforms, false, lp, double.NaN, initiatorMethionineBehavior, new List<string> { taskId }, false, 0, 0);
+                var analysisEngine = new AnalysisEngine(searchResults.OuterPsms, compactPeptideToProteinPeptideMatching, proteinList, variableModifications, fixedModifications, localizeableModifications, Protease, searchModes, myMsDataFile, ProductMassTolerance, (BinTreeStructure myTreeStructure, string s) => WriteTree(myTreeStructure, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, "Individual Searches", origDataFileName }), (List<NewPsmWithFdr> h, string s) => WritePsmsToTsv(h, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, "Individual Searches", origDataFileName }), null, false, false, MaxMissedCleavages, MaxModificationIsoforms, false, lp, double.NaN, initiatorMethionineBehavior, new List<string> { taskId, "Individual Searches", origDataFileName }, false, 0, 0);
 
                 var analysisResults = (AnalysisResults)analysisEngine.Run();
                 myTaskResults.AddResultText(analysisResults);
@@ -206,56 +207,58 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
 
                 // TODO: fix the tolerance calculation below
 
-                var a = new CalibrationEngine(myMsDataFile, ProductMassTolerance, identifications, minMS1isotopicPeaksNeededForConfirmedIdentification, minMS2isotopicPeaksNeededForConfirmedIdentification, numFragmentsNeededForEveryIdentification, PrecursorMassTolerance, fragmentTypesForCalibration, (List<LabeledMs1DataPoint> theList, string s) => WriteMs1DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, origDataFileName }), (List<LabeledMs2DataPoint> theList, string s) => WriteMs2DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, origDataFileName }), false, new List<string> { taskId });
+                var a = new CalibrationEngine(myMsDataFile, ProductMassTolerance, identifications, minMS1isotopicPeaksNeededForConfirmedIdentification, minMS2isotopicPeaksNeededForConfirmedIdentification, numFragmentsNeededForEveryIdentification, PrecursorMassTolerance, fragmentTypesForCalibration, (List<LabeledMs1DataPoint> theList, string s) => WriteMs1DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, "Individual Searches", origDataFileName }), (List<LabeledMs2DataPoint> theList, string s) => WriteMs2DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s, new List<string> { taskId, "Individual Searches", origDataFileName }), false, new List<string> { taskId, "Individual Searches", origDataFileName });
 
                 var resultBeforeFC = a.Run();
                 myTaskResults.AddResultText(resultBeforeFC);
 
                 // Second search round
 
                 var listOfSortedms2ScansTest = MyEngine.GetMs2Scans(myMsDataFile).OrderBy(b => b.MonoisotopicPrecursorMass).ToArray();
-                var searchEngineTest = new ClassicSearchEngine(listOfSortedms2ScansTest, myMsDataFile.NumSpectra, variableModifications, fixedModifications, proteinList, ProductMassTolerance, Protease, searchModes, MaxMissedCleavages, MaxModificationIsoforms, origDataFileName, lp, new List<string> { taskId });
+                var searchEngineTest = new ClassicSearchEngine(listOfSortedms2ScansTest, myMsDataFile.NumSpectra, variableModifications, fixedModifications, proteinList, ProductMassTolerance, Protease, searchModes, MaxMissedCleavages, MaxModificationIsoforms, origDataFileName, lp, new List<string> { taskId, "Individual Searches", origDataFileName });
                 var searchResultsTest = (ClassicSearchResults)searchEngineTest.Run();
                 myTaskResults.AddResultText(searchResultsTest);
-                var analysisEngineTest = new AnalysisEngine(searchResultsTest.OuterPsms, compactPeptideToProteinPeptideMatching, proteinList, variableModifications, fixedModifications, localizeableModifications, Protease, searchModes, myMsDataFile, ProductMassTolerance, (BinTreeStructure myTreeStructure, string s) => WriteTree(myTreeStructure, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test", new List<string> { taskId, origDataFileName }), (List<NewPsmWithFdr> h, string s) => WritePsmsToTsv(h, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test", new List<string> { taskId, origDataFileName }), null, false, false, MaxMissedCleavages, MaxModificationIsoforms, false, lp, double.NaN, initiatorMethionineBehavior, new List<string> { taskId }, false, 0, 0);
+                var analysisEngineTest = new AnalysisEngine(searchResultsTest.OuterPsms, compactPeptideToProteinPeptideMatching, proteinList, variableModifications, fixedModifications, localizeableModifications, Protease, searchModes, myMsDataFile, ProductMassTolerance, (BinTreeStructure myTreeStructure, string s) => WriteTree(myTreeStructure, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test", new List<string> { taskId, "Individual Searches", origDataFileName }), (List<NewPsmWithFdr> h, string s) => WritePsmsToTsv(h, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test", new List<string> { taskId, "Individual Searches", origDataFileName }), null, false, false, MaxMissedCleavages, MaxModificationIsoforms, false, lp, double.NaN, initiatorMethionineBehavior, new List<string> { taskId, "Individual Searches", origDataFileName }, false, 0, 0);
                 var analysisResultsTest = (AnalysisResults)analysisEngineTest.Run();
                 myTaskResults.AddResultText(analysisResultsTest);
 
                 //
 
-                var resultAfterFC = new CalibrationEngine(myMsDataFile, ProductMassTolerance, analysisResultsTest.AllResultingIdentifications[0], minMS1isotopicPeaksNeededForConfirmedIdentification, minMS2isotopicPeaksNeededForConfirmedIdentification, numFragmentsNeededForEveryIdentification, PrecursorMassTolerance, fragmentTypesForCalibration, (List<LabeledMs1DataPoint> theList, string s) => WriteMs1DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "after", new List<string> { taskId, origDataFileName }), (List<LabeledMs2DataPoint> theList, string s) => WriteMs2DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "after", new List<string> { taskId, origDataFileName }), true, new List<string> { taskId }).Run();
+                var resultAfterFC = new CalibrationEngine(myMsDataFile, ProductMassTolerance, analysisResultsTest.AllResultingIdentifications[0], minMS1isotopicPeaksNeededForConfirmedIdentification, minMS2isotopicPeaksNeededForConfirmedIdentification, numFragmentsNeededForEveryIdentification, PrecursorMassTolerance, fragmentTypesForCalibration, (List<LabeledMs1DataPoint> theList, string s) => WriteMs1DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "after", new List<string> { taskId, "Individual Searches", origDataFileName }), (List<LabeledMs2DataPoint> theList, string s) => WriteMs2DataPoints(theList, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "after", new List<string> { taskId, "Individual Searches", origDataFileName }), true, new List<string> { taskId, "Individual Searches", origDataFileName }).Run();
                 myTaskResults.AddResultText(resultAfterFC);
 
                 // Final search round - not required
 
                 var listOfSortedms2ScansTest2 = MyEngine.GetMs2Scans(myMsDataFile).OrderBy(b => b.MonoisotopicPrecursorMass).ToArray();
-                var searchEngineTest2 = new ClassicSearchEngine(listOfSortedms2ScansTest2, myMsDataFile.NumSpectra, variableModifications, fixedModifications, proteinList, ProductMassTolerance, Protease, searchModes, MaxMissedCleavages, MaxModificationIsoforms, origDataFileName, lp, new List<string> { taskId });
+                var searchEngineTest2 = new ClassicSearchEngine(listOfSortedms2ScansTest2, myMsDataFile.NumSpectra, variableModifications, fixedModifications, proteinList, ProductMassTolerance, Protease, searchModes, MaxMissedCleavages, MaxModificationIsoforms, origDataFileName, lp, new List<string> { taskId, "Individual Searches", origDataFileName });
                 var searchResultsTest2 = (ClassicSearchResults)searchEngineTest2.Run();
                 myTaskResults.AddResultText(searchResultsTest2);
-                var analysisEngineTest2 = new AnalysisEngine(searchResultsTest2.OuterPsms, compactPeptideToProteinPeptideMatching, proteinList, variableModifications, fixedModifications, localizeableModifications, Protease, searchModes, myMsDataFile, ProductMassTolerance, (BinTreeStructure myTreeStructure, string s) => WriteTree(myTreeStructure, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test2", new List<string> { taskId, origDataFileName }), (List<NewPsmWithFdr> h, string s) => WritePsmsToTsv(h, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test2", new List<string> { taskId, origDataFileName }), null, false, false, MaxMissedCleavages, MaxModificationIsoforms, false, lp, double.NaN, initiatorMethionineBehavior, new List<string> { taskId }, false, 0, 0);
+                var analysisEngineTest2 = new AnalysisEngine(searchResultsTest2.OuterPsms, compactPeptideToProteinPeptideMatching, proteinList, variableModifications, fixedModifications, localizeableModifications, Protease, searchModes, myMsDataFile, ProductMassTolerance, (BinTreeStructure myTreeStructure, string s) => WriteTree(myTreeStructure, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test2", new List<string> { taskId, "Individual Searches", origDataFileName }), (List<NewPsmWithFdr> h, string s) => WritePsmsToTsv(h, OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + s + "test2", new List<string> { taskId, "Individual Searches", origDataFileName }), null, false, false, MaxMissedCleavages, MaxModificationIsoforms, false, lp, double.NaN, initiatorMethionineBehavior, new List<string> { taskId, "Individual Searches", origDataFileName }, false, 0, 0);
+
                 var analysisResultsTest2 = (AnalysisResults)analysisEngineTest2.Run();
                 myTaskResults.AddResultText(analysisResultsTest2);
 
                 //
 
                 if (resultBeforeFC is MyErroredResults)
                 {
-                    Warn(a.ToString(), new List<string> { taskId });
+                    Warn(a.ToString(), new List<string> { taskId, "Individual Searches", origDataFileName });
                 }
                 else
                 {
-                    Status("Creating _indexedmzMLConnection, putting data in it, and writing!", new List<string> { taskId });
+                    Status("Creating _indexedmzMLConnection, putting data in it, and writing!", new List<string> { taskId, "Individual Searches", origDataFileName });
                     var path = Path.Combine(OutputFolder, Path.GetFileNameWithoutExtension(origDataFileName) + "-Calibrated.mzML");
                     lock (lock2) // Lock because writing is sequential
                     {
                         MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, path);
 
-                        SucessfullyFinishedWritingFile(path, new List<string> { taskId, origDataFileName });
+                        SucessfullyFinishedWritingFile(path, new List<string> { taskId, "Individual Searches", origDataFileName });
 
                         myTaskResults.newSpectra.Add(path);
                     }
                 }
-                FinishedDataFile(origDataFileName, new List<string> { taskId });
+                FinishedDataFile(origDataFileName, new List<string> { taskId, "Individual Searches", origDataFileName });
+                Status("Done!", new List<string> { taskId, "Individual Searches", origDataFileName });
             }
             );
             return myTaskResults;