Merge pull request #181 from rmillikin/master

fasta

Author: stefanks

InternalLogicWithFileIO/CalibrationTask/CalibrationTask.cs

@@ -88,12 +88,13 @@ protected override MyResults RunSpecific()
             List<MorpheusModification> variableModifications = ListOfModListsForCalibration.Where(b => b.Variable).SelectMany(b => b.Mods).ToList();
             List<MorpheusModification> fixedModifications = ListOfModListsForCalibration.Where(b => b.Fixed).SelectMany(b => b.Mods).ToList();
             List<MorpheusModification> localizeableModifications = ListOfModListsForCalibration.Where(b => b.Localize).SelectMany(b => b.Mods).ToList();
+
             Dictionary<string, List<MorpheusModification>> identifiedModsInXML;
             HashSet<string> unidentifiedModStrings;
-            MatchXMLmodsToKnownMods(xmlDbFilenameList, localizeableModifications, out identifiedModsInXML, out unidentifiedModStrings);
+            MatchXMLmodsToKnownMods(dbFilenameList, localizeableModifications, out identifiedModsInXML, out unidentifiedModStrings);
 
             Status("Loading proteins...");
-            var proteinList = xmlDbFilenameList.SelectMany(b => GetProteins(true, identifiedModsInXML, b)).ToList();
+            var proteinList = dbFilenameList.SelectMany(b => GetProteins(true, identifiedModsInXML, b)).ToList();
 
             List<ProductType> lp = new List<ProductType>();
             FragmentTypes fragmentTypesForCalibration = FragmentTypes.None;

InternalLogicWithFileIO/EverythingRunner/EverythingRunnerEngine.cs

@@ -15,13 +15,13 @@ public class EverythingRunnerEngine : MyEngine
 
         private readonly List<MyTaskEngine> taskList;
         private List<string> currentRawDataFilenameList;
-        private List<XmlForTask> currentXmlDbFilenameList;
+        private List<DbForTask> currentXmlDbFilenameList;
 
         #endregion Private Fields
 
         #region Public Constructors
 
-        public EverythingRunnerEngine(List<MyTaskEngine> taskList, List<string> startingRawFilenameList, List<XmlForTask> startingXmlDbFilenameList) : base(0)
+        public EverythingRunnerEngine(List<MyTaskEngine> taskList, List<string> startingRawFilenameList, List<DbForTask> startingXmlDbFilenameList) : base(0)
         {
             this.taskList = taskList;
             currentRawDataFilenameList = startingRawFilenameList;
@@ -91,7 +91,7 @@ where currentRawDataFilenameList.All(f => f.StartsWith(possibleMatch, StringComp
                 if (!Directory.Exists(output_folder))
                     Directory.CreateDirectory(output_folder);
                 ok.OutputFolder = output_folder;
-                ok.xmlDbFilenameList = currentXmlDbFilenameList;
+                ok.dbFilenameList = currentXmlDbFilenameList;
                 ok.rawDataFilenameList = currentRawDataFilenameList;
 
                 var myTaskResults = (MyTaskResults)ok.Run();
@@ -129,7 +129,7 @@ private void NewSpectras(List<string> newSpectra)
             newSpectrasHandler?.Invoke(this, new StringListEventArgs(newSpectra));
         }
 
-        private void NewDBs(List<XmlForTask> newDatabases)
+        private void NewDBs(List<DbForTask> newDatabases)
         {
             newDbsHandler?.Invoke(this, new XmlForTaskListEventArgs(newDatabases));
         }

InternalLogicWithFileIO/EverythingRunner/XmlForTaskListEventArgs.cs

@@ -8,13 +8,13 @@ public class XmlForTaskListEventArgs : EventArgs
 
         #region Public Fields
 
-        public List<XmlForTask> newDatabases;
+        public List<DbForTask> newDatabases;
 
         #endregion Public Fields
 
         #region Public Constructors
 
-        public XmlForTaskListEventArgs(List<XmlForTask> newDatabases)
+        public XmlForTaskListEventArgs(List<DbForTask> newDatabases)
         {
             this.newDatabases = newDatabases;
         }

InternalLogicWithFileIO/GPTMDTask/GPTMDTask.cs

@@ -169,7 +169,7 @@ public static void WriteXmlDatabase(Dictionary<string, HashSet<Tuple<int, string
         protected override MyResults RunSpecific()
         {
             MyTaskResults myGPTMDresults = new MyGPTMDTaskResults(this);
-            myGPTMDresults.newDatabases = new List<XmlForTask>();
+            myGPTMDresults.newDatabases = new List<DbForTask>();
 
             var currentRawFileList = rawDataFilenameList;
 
@@ -180,9 +180,10 @@ protected override MyResults RunSpecific()
             List<MorpheusModification> fixedModifications = listOfModListsForGPTMD.Where(b => b.Fixed).SelectMany(b => b.Mods).ToList();
             List<MorpheusModification> localizeableModifications = listOfModListsForGPTMD.Where(b => b.Localize).SelectMany(b => b.Mods).ToList();
             List<MorpheusModification> gptmdModifications = listOfModListsForGPTMD.Where(b => b.Gptmd).SelectMany(b => b.Mods).ToList();
+
             Dictionary<string, List<MorpheusModification>> identifiedModsInXML;
             HashSet<string> unidentifiedModStrings;
-            MatchXMLmodsToKnownMods(xmlDbFilenameList, localizeableModifications, out identifiedModsInXML, out unidentifiedModStrings);
+            MatchXMLmodsToKnownMods(dbFilenameList, localizeableModifications, out identifiedModsInXML, out unidentifiedModStrings);
 
             IEnumerable<Tuple<double, double>> combos = LoadCombos().ToList();
 
@@ -200,7 +201,7 @@ protected override MyResults RunSpecific()
                 lp.Add(ProductType.Y);
 
             Status("Loading proteins...");
-            var proteinList = xmlDbFilenameList.SelectMany(b => GetProteins(true, identifiedModsInXML, b)).ToList();
+            var proteinList = dbFilenameList.SelectMany(b => GetProteins(true, identifiedModsInXML, b)).ToList();
             AnalysisEngine analysisEngine;
             AnalysisResults analysisResults = null;
             for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
@@ -240,14 +241,14 @@ protected override MyResults RunSpecific()
 
             //output(gptmdResults.ToString());
 
-            string outputXMLdbFullName = Path.Combine(OutputFolder, string.Join("-", xmlDbFilenameList.Select(b => Path.GetFileNameWithoutExtension(b.FileName))) + "GPTMD.xml");
+            string outputXMLdbFullName = Path.Combine(OutputFolder, string.Join("-", dbFilenameList.Select(b => Path.GetFileNameWithoutExtension(b.FileName))) + "GPTMD.xml");
 
             WriteXmlDatabase(gptmdResults.Mods, proteinList.Where(b => !b.IsDecoy).ToList(), outputXMLdbFullName);
 
             SucessfullyFinishedWritingFile(outputXMLdbFullName);
 
             // TODO: Fix so not always outputting a contaminant
-            myGPTMDresults.newDatabases.Add(new XmlForTask(outputXMLdbFullName, false));
+            myGPTMDresults.newDatabases.Add(new DbForTask(outputXMLdbFullName, false));
 
             return myGPTMDresults;
         }

InternalLogicWithFileIO/InternalLogicTaskLayer.csproj

@@ -97,7 +97,7 @@
     <Compile Include="GPTMDTask\GPTMDTask.cs" />
     <Compile Include="GPTMDTask\ModListForGPTMDTask.cs" />
     <Compile Include="CalibrationTask\ModListForCalibrationTask.cs" />
-    <Compile Include="Parent\XmlForTask.cs" />
+    <Compile Include="Parent\DbForTask.cs" />
     <Compile Include="SearchTask\ModListForSearchTask.cs" />
     <Compile Include="ModList.cs" />
     <Compile Include="SearchTask\MySearchTaskResults.cs" />

InternalLogicWithFileIO/Parent/XmlForTask.cs InternalLogicWithFileIO/Parent/DbForTask.cs

@@ -1,11 +1,11 @@
 namespace InternalLogicTaskLayer
 {
-    public class XmlForTask
+    public class DbForTask
     {
 
         #region Public Constructors
 
-        public XmlForTask(string fileName, bool isContaminant)
+        public DbForTask(string fileName, bool isContaminant)
         {
             FileName = fileName;
             IsContaminant = isContaminant;