From d1bc75c6aaccaf08c3d2c31318e1a6e58ea6684c Mon Sep 17 00:00:00 2001 From: Michael Shortreed <mshort@chem.wisc.edu> Date: Wed, 8 Nov 2023 14:01:30 -0600 Subject: [PATCH] moved fragmentation and library spectrum to new project Omics --- mzLib/Omics/Class1.cs | 7 ++ .../DissociationTypeCollection.cs | 5 +- .../Fragmentation/FragmentationTerminus.cs | 2 +- .../Fragmentation/MatchedFragmentIon.cs | 6 +- .../Fragmentation/Product.cs | 5 +- .../Fragmentation/ProductType.cs | 4 +- .../TerminusSpecificProductTypes.cs | 6 +- .../PSM => Omics}/LibrarySpectrum.cs | 11 +- mzLib/Omics/Omics.csproj | 15 +++ mzLib/Proteomics/PSM/PsmFromTsv.cs | 3 +- mzLib/Proteomics/Protein/Protein.cs | 4 +- .../ProteolyticDigestion/DigestionParams.cs | 4 +- .../PeptideWithSetModifications.cs | 6 +- .../ProductTypeMethods.cs | 4 +- .../ProteaseDictionary.cs | 1 - .../ProteolyticDigestion/ProteinDigestion.cs | 2 +- mzLib/Proteomics/Proteomics.csproj | 1 + .../DatabaseTests/TestProteomicsReadWrite.cs | 2 +- mzLib/Test/Test.csproj | 1 + mzLib/Test/TestDigestionMotif.cs | 4 +- mzLib/Test/TestFragments.cs | 3 +- mzLib/Test/TestLibrarySpectrum.cs | 3 +- mzLib/Test/TestModifications.cs | 2 +- mzLib/Test/TestPeptideWithSetMods.cs | 2 +- mzLib/Test/TestPeptides.cs | 2 +- .../TestProductMassesMightHaveDuplicates.cs | 2 +- mzLib/Test/TestProteinDigestion.cs | 2 +- mzLib/Test/TestPsmFromTsv.cs | 2 +- mzLib/mzLib.sln | 107 ++++++++++++++++++ 29 files changed, 168 insertions(+), 50 deletions(-) create mode 100644 mzLib/Omics/Class1.cs rename mzLib/{Proteomics => Omics}/Fragmentation/DissociationTypeCollection.cs (98%) rename mzLib/{Proteomics => Omics}/Fragmentation/FragmentationTerminus.cs (85%) rename mzLib/{Proteomics => Omics}/Fragmentation/MatchedFragmentIon.cs (97%) rename mzLib/{Proteomics => Omics}/Fragmentation/Product.cs (98%) rename mzLib/{Proteomics => Omics}/Fragmentation/ProductType.cs (94%) rename mzLib/{Proteomics => Omics}/Fragmentation/TerminusSpecificProductTypes.cs (95%) rename mzLib/{Proteomics/PSM => Omics}/LibrarySpectrum.cs (95%) create mode 100644 mzLib/Omics/Omics.csproj diff --git a/mzLib/Omics/Class1.cs b/mzLib/Omics/Class1.cs new file mode 100644 index 000000000..141e484ab --- /dev/null +++ b/mzLib/Omics/Class1.cs @@ -0,0 +1,7 @@ +namespace Omics +{ + public class Class1 + { + + } +} \ No newline at end of file diff --git a/mzLib/Proteomics/Fragmentation/DissociationTypeCollection.cs b/mzLib/Omics/Fragmentation/DissociationTypeCollection.cs similarity index 98% rename from mzLib/Proteomics/Fragmentation/DissociationTypeCollection.cs rename to mzLib/Omics/Fragmentation/DissociationTypeCollection.cs index 63167105b..4fa02b178 100644 --- a/mzLib/Proteomics/Fragmentation/DissociationTypeCollection.cs +++ b/mzLib/Omics/Fragmentation/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/mzLib/Proteomics/Fragmentation/FragmentationTerminus.cs b/mzLib/Omics/Fragmentation/FragmentationTerminus.cs similarity index 85% rename from mzLib/Proteomics/Fragmentation/FragmentationTerminus.cs rename to mzLib/Omics/Fragmentation/FragmentationTerminus.cs index 84e8958f8..4c5acfc47 100644 --- a/mzLib/Proteomics/Fragmentation/FragmentationTerminus.cs +++ b/mzLib/Omics/Fragmentation/FragmentationTerminus.cs @@ -1,4 +1,4 @@ -namespace Proteomics.Fragmentation +namespace Omics.Fragmentation { public enum FragmentationTerminus { diff --git a/mzLib/Proteomics/Fragmentation/MatchedFragmentIon.cs b/mzLib/Omics/Fragmentation/MatchedFragmentIon.cs similarity index 97% rename from mzLib/Proteomics/Fragmentation/MatchedFragmentIon.cs rename to mzLib/Omics/Fragmentation/MatchedFragmentIon.cs index 81de97f24..59ba74656 100644 --- a/mzLib/Proteomics/Fragmentation/MatchedFragmentIon.cs +++ b/mzLib/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 b/mzLib/Omics/Fragmentation/Product.cs similarity index 98% rename from mzLib/Proteomics/Fragmentation/Product.cs rename to mzLib/Omics/Fragmentation/Product.cs index 1b8ed9f97..876ee7125 100644 --- a/mzLib/Proteomics/Fragmentation/Product.cs +++ b/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/mzLib/Proteomics/Fragmentation/ProductType.cs b/mzLib/Omics/Fragmentation/ProductType.cs similarity index 94% rename from mzLib/Proteomics/Fragmentation/ProductType.cs rename to mzLib/Omics/Fragmentation/ProductType.cs index 2b3a84112..e10b0a74c 100644 --- a/mzLib/Proteomics/Fragmentation/ProductType.cs +++ b/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/mzLib/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs b/mzLib/Omics/Fragmentation/TerminusSpecificProductTypes.cs similarity index 95% rename from mzLib/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs rename to mzLib/Omics/Fragmentation/TerminusSpecificProductTypes.cs index 054fcc745..3cd751543 100644 --- a/mzLib/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs +++ b/mzLib/Omics/Fragmentation/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 b/mzLib/Omics/LibrarySpectrum.cs similarity index 95% rename from mzLib/Proteomics/PSM/LibrarySpectrum.cs rename to mzLib/Omics/LibrarySpectrum.cs index 5301f72a7..4b5c62a9b 100644 --- a/mzLib/Proteomics/PSM/LibrarySpectrum.cs +++ b/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 new file mode 100644 index 000000000..a65efa0cf --- /dev/null +++ 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 index c6fef635c..d432fa38f 100644 --- 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 index aec1d7998..b16050ec3 100644 --- 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 index 45ef76701..2fbbf50fc 100644 --- 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 index 067afb849..d62441313 100644 --- 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 index 642052f41..bb2c74b07 100644 --- 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 index a52955f0d..ef3a3352d 100644 --- 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 index 668dec2a8..caea1494c 100644 --- 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 index 5b87fbed8..efaaf0c40 100644 --- 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 index cc7613f5a..20850a3ac 100644 --- 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 index aa76dfad0..a295d07e1 100644 --- 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 index c58d9e63b..ddf12783a 100644 --- 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 index 9bbdfe6ba..d617a027f 100644 --- 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 index daa1cba38..98f79fd54 100644 --- 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 index 725da2931..b46eaaf65 100644 --- 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 index 7deb0a871..8ab0623a4 100644 --- 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 index 8009b1ca3..492866aa5 100644 --- 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 index 18dc5b6f0..a04bf00fd 100644 --- 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 index 46520cfd8..8780b6df4 100644 --- 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 index fa5b2afee..71b6bb30c 100644 --- a/mzLib/Test/TestPsmFromTsv.cs +++ b/mzLib/Test/TestPsmFromTsv.cs @@ -1,5 +1,4 @@ using NUnit.Framework; -using Proteomics.Fragmentation; using Proteomics.ProteolyticDigestion; using Proteomics.PSM; using System; @@ -7,6 +6,7 @@ using System.IO; using System.Linq; using System.Text.RegularExpressions; +using Omics.Fragmentation; using Proteomics; namespace Test diff --git a/mzLib/mzLib.sln b/mzLib/mzLib.sln index 8fd527182..32bc91fe3 100644 --- a/mzLib/mzLib.sln +++ b/mzLib/mzLib.sln @@ -33,102 +33,209 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Development", "Development\ EndProject Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Readers", "Readers\Readers.csproj", "{E27A5C14-0C05-466A-91CE-ABB5151A69C4}" EndProject +Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Omics", "Omics\Omics.csproj", "{C53C4AB3-D987-42D3-97EF-052863CDD4D8}" +EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution + Debug|Any CPU = Debug|Any CPU Debug|x64 = Debug|x64 + Release|Any CPU = Release|Any CPU Release|x64 = Release|x64 + TestAndRelease|Any CPU 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