Merge pull request #188 from smith-chem-wisc/StefanBranch

so many

Author: stefanks

.travis.yml

@@ -5,13 +5,13 @@ install:
 - nuget install NUnit.Console -OutputDirectory testrunner
 script:
 - echo $TRAVIS_TAG 
-- cat MetaMorpheusCommandLine/Properties/AssemblyInfo.cs
-- if [ -n "${TRAVIS_TAG}" ]; then sed -i -- 's/1.0.0.0/'$TRAVIS_TAG'/g' MetaMorpheusCommandLine/Properties/AssemblyInfo.cs ; fi
-- if [ -n "${TRAVIS_TAG}" ]; then sed -i -- 's/1.0.0.0/'$TRAVIS_TAG'/g' InternalLogic/Properties/AssemblyInfo.cs ; fi
-- cat MetaMorpheusCommandLine/Properties/AssemblyInfo.cs
+- cat CMD/Properties/AssemblyInfo.cs
+- if [ -n "${TRAVIS_TAG}" ]; then sed -i -- 's/1.0.0.0/'$TRAVIS_TAG'/g' CMD/Properties/AssemblyInfo.cs ; fi
+- if [ -n "${TRAVIS_TAG}" ]; then sed -i -- 's/1.0.0.0/'$TRAVIS_TAG'/g' EngineLayer/Properties/AssemblyInfo.cs ; fi
+- cat CMD/Properties/AssemblyInfo.cs
 - xbuild /p:Configuration=TestAndReleaseTravis MetaMorpheus.sln
 - mono ./testrunner/NUnit.ConsoleRunner.*/tools/nunit3-console.exe ./Test/bin/Release/Test.dll
-- tar -zcvf MonoCommandLine.tar.gz -C MetaMorpheusCommandLine/bin/Release .
+- tar -zcvf MonoCommandLine.tar.gz -C CMD/bin/Release .
 deploy:
   provider: releases
   api_key:

MetaMorpheusCommandLine/App.config CMD/App.config

@@ -1,14 +1,14 @@
-<?xml version="1.0" encoding="utf-8"?>
-<configuration>
-  <startup>
-    <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.5.1" />
-  </startup>
-  <runtime>
-    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
-      <dependentAssembly>
-        <assemblyIdentity name="FSharp.Core" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-4.4.0.0" newVersion="4.4.0.0" />
-      </dependentAssembly>
-    </assemblyBinding>
-  </runtime>
+<?xml version="1.0" encoding="utf-8"?>
+<configuration>
+  <startup>
+    <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.5.1" />
+  </startup>
+  <runtime>
+    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
+      <dependentAssembly>
+        <assemblyIdentity name="FSharp.Core" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
+        <bindingRedirect oldVersion="0.0.0.0-4.4.0.0" newVersion="4.4.0.0" />
+      </dependentAssembly>
+    </assemblyBinding>
+  </runtime>
 </configuration>

MetaMorpheusCommandLine/MetaMorpheusCommandLine.csproj CMD/CMD.csproj

@@ -100,17 +100,13 @@
     <None Include="packages.config" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\InternalLogicWithFileIO\InternalLogicTaskLayer.csproj">
+    <ProjectReference Include="..\TaskLayer\TaskLayer.csproj">
       <Project>{04B0EE7D-5FD3-47A5-ABAA-658D177E4229}</Project>
-      <Name>InternalLogicTaskLayer</Name>
+      <Name>TaskLayer</Name>
     </ProjectReference>
-    <ProjectReference Include="..\InternalLogic\InternalLogicEngineLayer.csproj">
+    <ProjectReference Include="..\EngineLayer\EngineLayer.csproj">
       <Project>{A9A105AF-E6C4-40E8-AA7D-5E6FAB72542A}</Project>
-      <Name>InternalLogicEngineLayer</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\OldInternalLogic\OldInternalLogic.csproj">
-      <Project>{d2178d2e-7cbd-48a3-835d-8b13872202ff}</Project>
-      <Name>OldInternalLogic</Name>
+      <Name>EngineLayer</Name>
     </ProjectReference>
   </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />

MetaMorpheusCommandLine/Program.cs CMD/Program.cs

@@ -1,12 +1,6 @@
-using InternalLogicEngineLayer;
-using InternalLogicTaskLayer;
-using IO.MzML;
-using MassSpectrometry;
-using Spectra;
+using EngineLayer;
 using System;
-using System.Collections.Generic;
-using System.IO;
-using System.Linq;
+using TaskLayer;
 
 namespace MetaMorpheusCommandLine
 {
@@ -47,9 +41,8 @@ private static void Main(string[] args)
             MyTaskEngine.FinishedSingleTaskHandler += MyTaskEngine_finishedSingleTaskHandler;
             MyTaskEngine.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;
             MyTaskEngine.StartingSingleTaskHander += MyTaskEngine_startingSingleTaskHander;
-            
         }
-        
+
         private static void MyTaskEngine_startingSingleTaskHander(object sender, SingleTaskEventArgs e)
         {
             if (inProgress)

MetaMorpheusCommandLine/Properties/AssemblyInfo.cs CMD/Properties/AssemblyInfo.cs

@@ -1,35 +1,35 @@
-using System.Reflection;
-using System.Runtime.InteropServices;
-
-// General Information about an assembly is controlled through the following
-// set of attributes. Change these attribute values to modify the information
-// associated with an assembly.
-[assembly: AssemblyTitle("MetaMorpheusCommandLine")]
-[assembly: AssemblyDescription("")]
-[assembly: AssemblyConfiguration("")]
-[assembly: AssemblyCompany("")]
-[assembly: AssemblyProduct("MetaMorpheusCommandLine")]
-[assembly: AssemblyCopyright("Copyright ©  2016")]
-[assembly: AssemblyTrademark("")]
-[assembly: AssemblyCulture("")]
-
-// Setting ComVisible to false makes the types in this assembly not visible
-// to COM components.  If you need to access a type in this assembly from
-// COM, set the ComVisible attribute to true on that type.
-[assembly: ComVisible(false)]
-
-// The following GUID is for the ID of the typelib if this project is exposed to COM
-[assembly: Guid("dd89ef8c-a47a-4c6b-97bf-01b81d48847c")]
-
-// Version information for an assembly consists of the following four values:
-//
-//      Major Version
-//      Minor Version
-//      Build Number
-//      Revision
-//
-// You can specify all the values or you can default the Build and Revision Numbers
-// by using the '*' as shown below:
-// [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("1.0.0.0")]
+using System.Reflection;
+using System.Runtime.InteropServices;
+
+// General Information about an assembly is controlled through the following
+// set of attributes. Change these attribute values to modify the information
+// associated with an assembly.
+[assembly: AssemblyTitle("MetaMorpheusCommandLine")]
+[assembly: AssemblyDescription("")]
+[assembly: AssemblyConfiguration("")]
+[assembly: AssemblyCompany("")]
+[assembly: AssemblyProduct("MetaMorpheusCommandLine")]
+[assembly: AssemblyCopyright("Copyright ©  2016")]
+[assembly: AssemblyTrademark("")]
+[assembly: AssemblyCulture("")]
+
+// Setting ComVisible to false makes the types in this assembly not visible
+// to COM components.  If you need to access a type in this assembly from
+// COM, set the ComVisible attribute to true on that type.
+[assembly: ComVisible(false)]
+
+// The following GUID is for the ID of the typelib if this project is exposed to COM
+[assembly: Guid("dd89ef8c-a47a-4c6b-97bf-01b81d48847c")]
+
+// Version information for an assembly consists of the following four values:
+//
+//      Major Version
+//      Minor Version
+//      Build Number
+//      Revision
+//
+// You can specify all the values or you can default the Build and Revision Numbers
+// by using the '*' as shown below:
+// [assembly: AssemblyVersion("1.0.*")]
+[assembly: AssemblyVersion("1.0.0.0")]
 [assembly: AssemblyFileVersion("1.0.0.0")]

InternalLogicWithFileIO/packages.config CMD/packages.config

@@ -1,5 +1,4 @@
 using MassSpectrometry;
-using OldInternalLogic;
 using Proteomics;
 using Spectra;
 using System;
@@ -9,7 +8,7 @@
 using System.Linq;
 using System.Threading.Tasks;
 
-namespace InternalLogicEngineLayer
+namespace EngineLayer.Analysis
 {
     public class AnalysisEngine : MyEngine
     {
@@ -20,11 +19,11 @@ public class AnalysisEngine : MyEngine
         private readonly double binTol;
         private readonly int maximumMissedCleavages;
         private readonly int maxModIsoforms;
-        private readonly ParentSpectrumMatch[][] newPsms;
+        private readonly PsmParent[][] newPsms;
         private readonly List<Protein> proteinList;
-        private readonly List<MorpheusModification> variableModifications;
-        private readonly List<MorpheusModification> fixedModifications;
-        private readonly List<MorpheusModification> localizeableModifications;
+        private readonly List<MetaMorpheusModification> variableModifications;
+        private readonly List<MetaMorpheusModification> fixedModifications;
+        private readonly List<MetaMorpheusModification> localizeableModifications;
         private readonly Protease protease;
         private readonly List<SearchMode> searchModes;
         private readonly IMsDataFile<IMzSpectrum<MzPeak>> myMsDataFile;
@@ -41,7 +40,7 @@ public class AnalysisEngine : MyEngine
 
         #region Public Constructors
 
-        public AnalysisEngine(ParentSpectrumMatch[][] newPsms, Dictionary<CompactPeptide, HashSet<PeptideWithSetModifications>> compactPeptideToProteinPeptideMatching, List<Protein> proteinList, List<MorpheusModification> variableModifications, List<MorpheusModification> fixedModifications, List<MorpheusModification> localizeableModifications, Protease protease, List<SearchMode> searchModes, IMsDataFile<IMzSpectrum<MzPeak>> myMSDataFile, Tolerance fragmentTolerance, Action<BinTreeStructure, string> action1, Action<List<NewPsmWithFdr>, string> action2, Action<List<ProteinGroup>, string> action3, bool doParsimony, int maximumMissedCleavages, int maxModIsoforms, bool doHistogramAnalysis, List<ProductType> lp, double binTol) : base(2)
+        public AnalysisEngine(PsmParent[][] newPsms, Dictionary<CompactPeptide, HashSet<PeptideWithSetModifications>> compactPeptideToProteinPeptideMatching, List<Protein> proteinList, List<MetaMorpheusModification> variableModifications, List<MetaMorpheusModification> fixedModifications, List<MetaMorpheusModification> localizeableModifications, Protease protease, List<SearchMode> searchModes, IMsDataFile<IMzSpectrum<MzPeak>> myMSDataFile, Tolerance fragmentTolerance, Action<BinTreeStructure, string> action1, Action<List<NewPsmWithFdr>, string> action2, Action<List<ProteinGroup>, string> action3, bool doParsimony, int maximumMissedCleavages, int maxModIsoforms, bool doHistogramAnalysis, List<ProductType> lp, double binTol) : base(2)
         {
             this.doParsimony = doParsimony;
             this.doHistogramAnalysis = doHistogramAnalysis;
@@ -605,12 +604,12 @@ protected override MyResults RunSpecific()
             {
                 if (newPsms[j] != null)
                 {
-                    PSMwithProteinHashSet[] psmsWithProteinHashSet = new PSMwithProteinHashSet[newPsms[0].Length];
+                    PsmWithMultiplePossiblePeptides[] psmsWithProteinHashSet = new PsmWithMultiplePossiblePeptides[newPsms[0].Length];
                     for (int i = 0; i < newPsms[0].Length; i++)
                     {
                         var huh = newPsms[j][i];
                         if (huh != null && huh.score >= 1)
-                            psmsWithProteinHashSet[i] = new PSMwithProteinHashSet(huh, compactPeptideToProteinPeptideMatching[huh.GetCompactPeptide(variableModifications, localizeableModifications, fixedModifications)], fragmentTolerance, myMsDataFile, lp);
+                            psmsWithProteinHashSet[i] = new PsmWithMultiplePossiblePeptides(huh, compactPeptideToProteinPeptideMatching[huh.GetCompactPeptide(variableModifications, localizeableModifications, fixedModifications)], fragmentTolerance, myMsDataFile, lp);
                     }
 
                     var orderedPsmsWithPeptides = psmsWithProteinHashSet.Where(b => b != null).OrderByDescending(b => b.Score);
@@ -682,7 +681,7 @@ private static void IdentifyFracWithSingle(BinTreeStructure myTreeStructure)
         {
             foreach (Bin bin in myTreeStructure.FinalBins)
             {
-                bin.FracWithSingle = (double)bin.uniquePSMs.Values.Where(b => !b.Item3.IsDecoy && b.Item3.thisPSM.peptidesWithSetModifications.Count == 1).Count() / bin.uniquePSMs.Values.Where(b => !b.Item3.IsDecoy).Count();
+                bin.FracWithSingle = (double)bin.uniquePSMs.Values.Count(b => !b.Item3.IsDecoy && b.Item3.thisPSM.peptidesWithSetModifications.Count == 1) / bin.uniquePSMs.Values.Count(b => !b.Item3.IsDecoy);
             }
         }
 
@@ -931,16 +930,18 @@ private static BinTreeStructure MyAnalysis(List<NewPsmWithFdr> limitedpsms_with_
 
             OverlappingIonSequences(myTreeStructure);
 
+            IdentifyFracWithSingle(myTreeStructure);
+
             return myTreeStructure;
         }
 
-        private static List<NewPsmWithFdr> DoFalseDiscoveryRateAnalysis(IEnumerable<PSMwithProteinHashSet> items)
+        private static List<NewPsmWithFdr> DoFalseDiscoveryRateAnalysis(IEnumerable<PsmWithMultiplePossiblePeptides> items)
         {
             var ids = new List<NewPsmWithFdr>();
 
             int cumulative_target = 0;
             int cumulative_decoy = 0;
-            foreach (PSMwithProteinHashSet item in items)
+            foreach (PsmWithMultiplePossiblePeptides item in items)
             {
                 var isDecoy = item.IsDecoy;
                 if (isDecoy)
@@ -1038,5 +1039,28 @@ private void AddObservedPeptidesToDictionary()
 
         #endregion Private Methods
 
+        #region Private Classes
+
+        private class SequenceComparer : IEqualityComparer<PsmWithMultiplePossiblePeptides>
+        {
+
+            #region Public Methods
+
+            public bool Equals(PsmWithMultiplePossiblePeptides x, PsmWithMultiplePossiblePeptides y)
+            {
+                return x.FullSequence.Equals(y.FullSequence);
+            }
+
+            public int GetHashCode(PsmWithMultiplePossiblePeptides obj)
+            {
+                return obj.FullSequence.GetHashCode();
+            }
+
+            #endregion Public Methods
+
+        }
+
+        #endregion Private Classes
+
     }
 }

InternalLogic/AnalysisEngine.cs EngineLayer/Analysis/AnalysisEngine.cs

@@ -2,7 +2,7 @@
 using System.Linq;
 using System.Text;
 
-namespace InternalLogicEngineLayer
+namespace EngineLayer.Analysis
 {
     public class AnalysisResults : MyResults
     {
@@ -34,7 +34,7 @@ protected override string StringForOutput
                 sb.Append("\t\tAll PSMS within 1% FDR: " + string.Join(", ", AllResultingIdentifications.Select(b => b.Count(c => c.qValue <= 0.01))));
 
                 if (ProteinGroups != null)
-                sb.Append("\n\t\tAll proteins within 1% FDR: " + string.Join(", ", ProteinGroups.Count(c => ((c.QValue <= 0.01) && (c.isDecoy == false)))));
+                    sb.Append("\n\t\tAll proteins within 1% FDR: " + string.Join(", ", ProteinGroups.Count(c => ((c.QValue <= 0.01) && (c.isDecoy == false)))));
 
                 return sb.ToString();
             }
@@ -43,4 +43,4 @@ protected override string StringForOutput
         #endregion Protected Properties
 
     }
-}
+}

InternalLogic/AnalysisResults.cs EngineLayer/Analysis/AnalysisResults.cs

@@ -2,7 +2,7 @@
 using System.Collections.Generic;
 using System.Linq;
 
-namespace InternalLogicEngineLayer
+namespace EngineLayer.Analysis
 {
     public class Bin
     {

InternalLogic/Bin.cs EngineLayer/Analysis/Bin.cs

@@ -2,7 +2,7 @@
 using System.Collections.Generic;
 using System.Linq;
 
-namespace InternalLogicEngineLayer
+namespace EngineLayer.Analysis
 {
     public class BinTreeStructure
     {

InternalLogic/BinTreeStructure.cs EngineLayer/Analysis/BinTreeStructure.cs

@@ -1,15 +1,29 @@
-namespace InternalLogicEngineLayer
+namespace EngineLayer.Analysis
 {
     internal class MyInfo
     {
+
+        #region Internal Fields
+
         internal string infostring;
 
+        #endregion Internal Fields
+
+        #region Public Constructors
+
         public MyInfo(double MassShift, string infostring)
         {
             this.MassShift = MassShift;
             this.infostring = infostring;
         }
 
+        #endregion Public Constructors
+
+        #region Public Properties
+
         public double MassShift { get; internal set; }
+
+        #endregion Public Properties
+
     }
 }

InternalLogic/MyInfo.cs EngineLayer/Analysis/MyInfo.cs

@@ -1,4 +1,4 @@
-namespace InternalLogicEngineLayer
+namespace EngineLayer.Analysis
 {
     internal class OkBin
     {