Merge pull request #227 from smith-chem-wisc/StefanBranch

okay!

Author: stefanks

CMD/CMD.csproj

@@ -35,40 +35,40 @@
     <TreatWarningsAsErrors>true</TreatWarningsAsErrors>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="Chemistry, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\Chemistry.dll</HintPath>
+    <Reference Include="Chemistry, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\Chemistry.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="MassSpectrometry, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\MassSpectrometry.dll</HintPath>
+    <Reference Include="MassSpectrometry, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\MassSpectrometry.dll</HintPath>
       <Private>True</Private>
     </Reference>
     <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="mzIdentML, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\mzIdentML.dll</HintPath>
+    <Reference Include="mzIdentML, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\mzIdentML.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="MzLibUtil, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\MzLibUtil.dll</HintPath>
+    <Reference Include="MzLibUtil, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\MzLibUtil.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="MzML, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\MzML.dll</HintPath>
+    <Reference Include="MzML, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\MzML.dll</HintPath>
       <Private>True</Private>
     </Reference>
     <Reference Include="NetSerializer, Version=4.1.0.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\packages\NetSerializer.4.1.0\lib\net45\NetSerializer.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="Proteomics, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\Proteomics.dll</HintPath>
+    <Reference Include="Proteomics, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\Proteomics.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="Spectra, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\Spectra.dll</HintPath>
+    <Reference Include="Spectra, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\Spectra.dll</HintPath>
       <Private>True</Private>
     </Reference>
     <Reference Include="System" />
@@ -80,12 +80,12 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
-    <Reference Include="Thermo, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\Thermo.dll</HintPath>
+    <Reference Include="Thermo, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\Thermo.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="UsefulProteomicsDatabases, Version=1.0.97.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.97\lib\UsefulProteomicsDatabases.dll</HintPath>
+    <Reference Include="UsefulProteomicsDatabases, Version=1.0.103.0, Culture=neutral, processorArchitecture=AMD64">
+      <HintPath>..\packages\mzLib.1.0.103\lib\UsefulProteomicsDatabases.dll</HintPath>
       <Private>True</Private>
     </Reference>
     <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">

CMD/packages.config

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
   <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
-  <package id="mzLib" version="1.0.97" targetFramework="net451" />
+  <package id="mzLib" version="1.0.103" targetFramework="net451" />
   <package id="NetSerializer" version="4.1.0" targetFramework="net451" />
   <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
 </packages>

EngineLayer/Analysis/AnalysisEngine.cs

@@ -634,7 +634,7 @@ protected override MyResults RunSpecific()
                     else
                     {
                         Status("Running FDR analysis on unique peptides...");
-                        writePsmsAction(DoFalseDiscoveryRateAnalysis(orderedPsmsWithPeptides.GroupBy(b => b.FullSequence).FirstOrDefault(), searchModes[j]), "uniquePeptides" + searchModes[j].FileNameAddition);
+                        writePsmsAction(DoFalseDiscoveryRateAnalysis(orderedPsmsWithPeptides.GroupBy(b => b.FullSequence).Select(b => b.FirstOrDefault()), searchModes[j]), "uniquePeptides" + searchModes[j].FileNameAddition);
                     }
 
                     if (doParsimony)