moved fragmentation and library spectrum to new project Omics

smith-chem-wisc · Nov 8, 2023 · d1bc75c · d1bc75c
1 parent 74b80ad
commit d1bc75c
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Showing 29 changed files with 168 additions and 50 deletions.
diff --git a/mzLib/Omics/Class1.cs b/mzLib/Omics/Class1.cs
@@ -0,0 +1,7 @@
+namespace Omics
+{
+    public class Class1
+    {
+
+    }
+}
diff --git a/...agmentation/DissociationTypeCollection.cs → ...agmentation/DissociationTypeCollection.cs b/...agmentation/DissociationTypeCollection.cs → ...agmentation/DissociationTypeCollection.cs
@@ -1,10 +1,7 @@
 using Chemistry;
-using Easy.Common.Extensions;
 using MassSpectrometry;
-using System.Collections.Generic;
-using System.Linq;
 
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public class DissociationTypeCollection
     {

diff --git a/...cs/Fragmentation/FragmentationTerminus.cs → ...cs/Fragmentation/FragmentationTerminus.cs b/...cs/Fragmentation/FragmentationTerminus.cs → ...cs/Fragmentation/FragmentationTerminus.cs
@@ -1,4 +1,4 @@
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public enum FragmentationTerminus
     {

diff --git a/...omics/Fragmentation/MatchedFragmentIon.cs → ...Omics/Fragmentation/MatchedFragmentIon.cs b/...omics/Fragmentation/MatchedFragmentIon.cs → ...Omics/Fragmentation/MatchedFragmentIon.cs
@@ -1,7 +1,7 @@
-using Chemistry;
-using System.Text;
+using System.Text;
+using Chemistry;
 
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public class MatchedFragmentIon
     {

diff --git a/mzLib/Proteomics/Fragmentation/Product.cs → mzLib/Omics/Fragmentation/Product.cs b/mzLib/Proteomics/Fragmentation/Product.cs → mzLib/Omics/Fragmentation/Product.cs
@@ -1,7 +1,6 @@
-using System;
-using System.Text;
+using System.Text;
 
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public struct Product
     {

diff --git a/...b/Proteomics/Fragmentation/ProductType.cs → mzLib/Omics/Fragmentation/ProductType.cs b/...b/Proteomics/Fragmentation/ProductType.cs → mzLib/Omics/Fragmentation/ProductType.cs
@@ -1,6 +1,4 @@
-using System.Collections.Generic;
-
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public enum ProductType
     {

diff --git a/...mentation/TerminusSpecificProductTypes.cs → ...mentation/TerminusSpecificProductTypes.cs b/...mentation/TerminusSpecificProductTypes.cs → ...mentation/TerminusSpecificProductTypes.cs
@@ -1,8 +1,4 @@
-using System;
-using System.Collections.Generic;
-using System.Text;
-
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public class TerminusSpecificProductTypes
     {

diff --git a/mzLib/Proteomics/PSM/LibrarySpectrum.cs → mzLib/Omics/LibrarySpectrum.cs b/mzLib/Proteomics/PSM/LibrarySpectrum.cs → mzLib/Omics/LibrarySpectrum.cs
@@ -1,12 +1,9 @@
-using Easy.Common.Extensions;
+using System.Text;
+using Easy.Common.Extensions;
 using MassSpectrometry.MzSpectra;
-using Proteomics.Fragmentation;
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
+using Omics.Fragmentation;
 
-namespace Proteomics.PSM
+namespace Omics
 {
     public class LibrarySpectrum
     {

diff --git a/mzLib/Omics/Omics.csproj b/mzLib/Omics/Omics.csproj
@@ -0,0 +1,15 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>net6.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\Chemistry\Chemistry.csproj" />
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
+  </ItemGroup>
+
+</Project>
diff --git a/mzLib/Proteomics/PSM/PsmFromTsv.cs b/mzLib/Proteomics/PSM/PsmFromTsv.cs
@@ -1,6 +1,5 @@
 using Chemistry;
 using Easy.Common.Extensions;
-using Proteomics.Fragmentation;
 using System;
 using System.Collections.Generic;
 using System.Globalization;
@@ -9,6 +8,8 @@
 using System.Text;
 using System.Text.RegularExpressions;
 using System.Threading.Tasks;
+using Omics.Fragmentation;
+using Omics;
 
 namespace Proteomics.PSM
 {

diff --git a/mzLib/Proteomics/Protein/Protein.cs b/mzLib/Proteomics/Protein/Protein.cs
@@ -1,9 +1,9 @@
-using Proteomics.Fragmentation;
-using Proteomics.ProteolyticDigestion;
+using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
 using System.Text.RegularExpressions;
+using Omics.Fragmentation;
 
 namespace Proteomics
 {

diff --git a/mzLib/Proteomics/ProteolyticDigestion/DigestionParams.cs b/mzLib/Proteomics/ProteolyticDigestion/DigestionParams.cs
@@ -1,5 +1,5 @@
-using Proteomics.Fragmentation;
-using System;
+using System;
+using Omics.Fragmentation;
 
 namespace Proteomics.ProteolyticDigestion
 {

diff --git a/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs b/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs
@@ -1,13 +1,13 @@
  using Chemistry;
 using MassSpectrometry;
 using Proteomics.AminoAcidPolymer;
-using Proteomics.Fragmentation;
-using System;
+ using System;
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
+ using Omics.Fragmentation;
 
-namespace Proteomics.ProteolyticDigestion
+ namespace Proteomics.ProteolyticDigestion
 {
     [Serializable]
     public class PeptideWithSetModifications : ProteolyticPeptide

diff --git a/mzLib/Proteomics/ProteolyticDigestion/ProductTypeMethods.cs b/mzLib/Proteomics/ProteolyticDigestion/ProductTypeMethods.cs
@@ -1,6 +1,6 @@
-using Proteomics.Fragmentation;
-using System;
+using System;
 using System.Collections.Generic;
+using Omics.Fragmentation;
 
 namespace Proteomics.ProteolyticDigestion
 {

diff --git a/mzLib/Proteomics/ProteolyticDigestion/ProteaseDictionary.cs b/mzLib/Proteomics/ProteolyticDigestion/ProteaseDictionary.cs
@@ -4,7 +4,6 @@
 using System.IO;
 using System.Linq;
 using MzLibUtil;
-using Proteomics.Fragmentation;
 
 namespace Proteomics.ProteolyticDigestion
 {

diff --git a/mzLib/Proteomics/ProteolyticDigestion/ProteinDigestion.cs b/mzLib/Proteomics/ProteolyticDigestion/ProteinDigestion.cs
@@ -1,6 +1,6 @@
 using System.Collections.Generic;
 using System.Linq;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 
 namespace Proteomics.ProteolyticDigestion
 {

diff --git a/mzLib/Proteomics/Proteomics.csproj b/mzLib/Proteomics/Proteomics.csproj
@@ -14,6 +14,7 @@
     <ProjectReference Include="..\Chemistry\Chemistry.csproj" />
     <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
+    <ProjectReference Include="..\Omics\Omics.csproj" />
     <ProjectReference Include="..\PepXML\PepXML.csproj" />
   </ItemGroup>
 

diff --git a/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs b/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs
@@ -4,8 +4,8 @@
 using System.Linq;
 using MassSpectrometry;
 using NUnit.Framework;
+using Omics.Fragmentation;
 using Proteomics;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using UsefulProteomicsDatabases;
 using Stopwatch = System.Diagnostics.Stopwatch;

diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj
@@ -26,6 +26,7 @@
     <ProjectReference Include="..\FlashLFQ\FlashLFQ.csproj" />
     <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />
     <ProjectReference Include="..\MzIdentML\MzIdentML.csproj" />
+    <ProjectReference Include="..\Omics\Omics.csproj" />
     <ProjectReference Include="..\SpectralAveraging\SpectralAveraging.csproj" />
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
     <ProjectReference Include="..\mzPlot\mzPlot.csproj" />

diff --git a/mzLib/Test/TestDigestionMotif.cs b/mzLib/Test/TestDigestionMotif.cs
@@ -565,8 +565,8 @@ public static void TestProteolyticDigestion()
             //check that there are no duplicates
             Assert.IsTrue(pwsms.Count == hashset.Count);
             //Speedy semi specific test
-            DigestionParams speedySemiN = new DigestionParams("trypsin", 10, 29, 30, 1024, InitiatorMethionineBehavior.Retain, 2, CleavageSpecificity.Semi, Proteomics.Fragmentation.FragmentationTerminus.N);
-            DigestionParams speedySemiC = new DigestionParams("trypsin", 10, 29, 30, 1024, InitiatorMethionineBehavior.Retain, 2, CleavageSpecificity.Semi, Proteomics.Fragmentation.FragmentationTerminus.C);
+            DigestionParams speedySemiN = new DigestionParams("trypsin", 10, 29, 30, 1024, InitiatorMethionineBehavior.Retain, 2, CleavageSpecificity.Semi, Omics.Fragmentation.FragmentationTerminus.N);
+            DigestionParams speedySemiC = new DigestionParams("trypsin", 10, 29, 30, 1024, InitiatorMethionineBehavior.Retain, 2, CleavageSpecificity.Semi, Omics.Fragmentation.FragmentationTerminus.C);
             List<PeptideWithSetModifications> pwsmsN = humanInsulin.Digest(speedySemiN, null, null).ToList();
             List<PeptideWithSetModifications> pwsmsC = humanInsulin.Digest(speedySemiC, null, null).ToList();
             Assert.IsTrue(pwsmsN.Count == 7);

diff --git a/mzLib/Test/TestFragments.cs b/mzLib/Test/TestFragments.cs
@@ -23,12 +23,11 @@
 using NUnit.Framework;
 using Proteomics;
 using Proteomics.AminoAcidPolymer;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
-
+using Omics.Fragmentation;
 using Stopwatch = System.Diagnostics.Stopwatch;
 
 namespace Test

diff --git a/mzLib/Test/TestLibrarySpectrum.cs b/mzLib/Test/TestLibrarySpectrum.cs
@@ -1,11 +1,12 @@
 using NUnit.Framework;
-using Proteomics.Fragmentation;
 using Proteomics.PSM;
 using System;
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using Omics;
+using Omics.Fragmentation;
 
 namespace Test
 {

diff --git a/mzLib/Test/TestModifications.cs b/mzLib/Test/TestModifications.cs
@@ -22,12 +22,12 @@
 using NUnit.Framework;
 using Proteomics;
 using Proteomics.AminoAcidPolymer;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections;
 using System.Collections.Generic;
 using System.Linq;
+using Omics.Fragmentation;
 using UsefulProteomicsDatabases;
 using Stopwatch = System.Diagnostics.Stopwatch;
 

diff --git a/mzLib/Test/TestPeptideWithSetMods.cs b/mzLib/Test/TestPeptideWithSetMods.cs
@@ -1,12 +1,12 @@
 using Chemistry;
 using NUnit.Framework;
 using Proteomics;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
+using Omics.Fragmentation;
 using UsefulProteomicsDatabases;
 using Stopwatch = System.Diagnostics.Stopwatch;
 

diff --git a/mzLib/Test/TestPeptides.cs b/mzLib/Test/TestPeptides.cs
@@ -20,11 +20,11 @@
 using MzLibUtil;
 using NUnit.Framework;
 using Proteomics.AminoAcidPolymer;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using Omics.Fragmentation;
 using UsefulProteomicsDatabases;
 using Stopwatch = System.Diagnostics.Stopwatch;
 

diff --git a/mzLib/Test/TestProductMassesMightHaveDuplicates.cs b/mzLib/Test/TestProductMassesMightHaveDuplicates.cs
@@ -2,11 +2,11 @@
 using MassSpectrometry;
 using NUnit.Framework;
 using Proteomics;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using Omics.Fragmentation;
 using Stopwatch = System.Diagnostics.Stopwatch;
 
 namespace Test

diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs
@@ -3,12 +3,12 @@
 using NUnit.Framework;
 using Proteomics;
 using Proteomics.AminoAcidPolymer;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
+using Omics.Fragmentation;
 using UsefulProteomicsDatabases;
 using static Chemistry.PeriodicTable;
 using Stopwatch = System.Diagnostics.Stopwatch;

diff --git a/mzLib/Test/TestPsmFromTsv.cs b/mzLib/Test/TestPsmFromTsv.cs
@@ -1,12 +1,12 @@
 using NUnit.Framework;
-using Proteomics.Fragmentation;
 using Proteomics.ProteolyticDigestion;
 using Proteomics.PSM;
 using System;
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
 using System.Text.RegularExpressions;
+using Omics.Fragmentation;
 using Proteomics;
 
 namespace Test