From c9174eadc1ad57d8d1e28ae925464bf6c1897ab1 Mon Sep 17 00:00:00 2001 From: Alex Date: Mon, 12 Dec 2022 11:25:39 -0600 Subject: [PATCH] Changed MassSpectrometry.Proteomics* namespace back to Proteomics* --- mzLib/FlashLFQ/FlashLfqEngine.cs | 2 +- .../SpectralDeconvolutionAlgorithm.cs | 4 +- .../SpectralDeconvolutionParameters.cs | 4 +- .../MzSpectra/IsotopicEnvelope.cs | 2 +- .../AminoAcidPolymer/AminoAcidPolymer.cs | 2 +- .../AminoAcidPolymerExtensions.cs | 2 +- .../ChemicalFormulaFragment.cs | 2 +- .../ChemicalFormulaModification.cs | 2 +- .../ChemicalFormulaTerminus.cs | 2 +- .../AminoAcidPolymer/DigestionPoint.cs | 2 +- .../Proteomics/AminoAcidPolymer/Fragment.cs | 2 +- .../AminoAcidPolymer/FragmentTypes.cs | 2 +- .../Proteomics/AminoAcidPolymer/IProtease.cs | 2 +- .../ModificationCollection.cs | 2 +- .../AminoAcidPolymer/ModificationSites.cs | 2 +- .../AminoAcidPolymer/OldSchoolModification.cs | 2 +- ...olModificationWithMultiplePossibilities.cs | 2 +- .../Proteomics/AminoAcidPolymer/Peptide.cs | 2 +- .../Proteomics/AminoAcidPolymer/Residue.cs | 2 +- .../Proteomics/AminoAcidPolymer/Terminus.cs | 2 +- .../DissociationTypeCollection.cs | 3 +- .../Fragmentation/FragmentationTerminus.cs | 2 +- .../Fragmentation/MatchedFragmentIon.cs | 2 +- .../Proteomics/Fragmentation/Product.cs | 2 +- .../Proteomics/Fragmentation/ProductType.cs | 2 +- .../TerminusSpecificProductTypes.cs | 2 +- .../ModLocationOnPeptideOrProtein.cs | 2 +- .../Proteomics/Modifications/Modification.cs | 3 +- .../Modifications/ModificationLocalization.cs | 2 +- .../Modifications/ModificationMotif.cs | 2 +- .../Proteomics/Modifications/SilacLabel.cs | 2 +- .../Proteomics/Protein/DatabaseReference.cs | 2 +- .../Proteomics/Protein/DisulfideBond.cs | 2 +- .../Proteomics/Protein/Protein.cs | 8 +-- .../Protein/ProteoformLevelClassifier.cs | 4 +- .../Proteomics/Protein/ProteolysisProduct.cs | 2 +- .../Protein/SequenceVariantDescription.cs | 2 +- .../Proteomics/Protein/SequenceVariation.cs | 4 +- .../Proteomics/Protein/SnpEffAnnotation.cs | 2 +- .../Proteomics/Protein/SpliceSite.cs | 2 +- .../Proteomics/Protein/VariantApplication.cs | 4 +- .../CleavageSpecificity.cs | 2 +- .../ProteolyticDigestion/DigestionMotif.cs | 2 +- .../ProteolyticDigestion/DigestionParams.cs | 4 +- .../InitiatorMethionineBehavior.cs | 2 +- .../PeptideWithSetModifications.cs | 7 ++- .../ProductTypeMethods.cs | 4 +- .../ProteolyticDigestion/Protease.cs | 4 +- .../ProteaseDictionary.cs | 4 +- .../ProteolyticDigestion/ProteinDigestion.cs | 4 +- .../ProteolyticPeptide.cs | 4 +- .../Proteomics/RetentionTimePrediction/CZE.cs | 2 +- .../RetentionTimePrediction/SSRCalc3.cs | 4 +- .../RetentionTimePrediction/SeparationType.cs | 2 +- .../Test/DatabaseTests/TestDatabaseLoaders.cs | 2 +- mzLib/Test/DatabaseTests/TestProteinReader.cs | 2 +- .../DatabaseTests/TestProteomicsReadWrite.cs | 6 +- .../Test/DatabaseTests/TestVariantProtein.cs | 4 +- mzLib/Test/TestAminoAcids.cs | 2 +- mzLib/Test/TestDeconvolution.cs | 4 +- mzLib/Test/TestDigestionMotif.cs | 8 +-- mzLib/Test/TestFragments.cs | 8 +-- mzLib/Test/TestIsolation.cs | 2 +- mzLib/Test/TestIsotopicEnvelope.cs | 4 +- mzLib/Test/TestModFits.cs | 2 +- mzLib/Test/TestModifications.cs | 8 +-- mzLib/Test/TestMsDataFile.cs | 6 +- mzLib/Test/TestMzML.cs | 2 +- mzLib/Test/TestPeptideWithSetMods.cs | 6 +- mzLib/Test/TestPeptides.cs | 6 +- .../TestProductMassesMightHaveDuplicates.cs | 6 +- mzLib/Test/TestProteinDatabase.cs | 2 +- mzLib/Test/TestProteinDigestion.cs | 8 +-- mzLib/Test/TestProteinProperties.cs | 2 +- mzLib/Test/TestPtmListLoader.cs | 2 +- mzLib/Test/TestRetentionTimePrediction.cs | 6 +- mzLib/Test/TestSeqCoverage.cs | 4 +- mzLib/TestFlashLFQ/TestFlashLFQ.cs | 60 +++++++++---------- .../DecoyProteinGenerator.cs | 2 +- mzLib/UsefulProteomicsDatabases/Loaders.cs | 2 +- .../ProteinDbLoader.cs | 4 +- .../ProteinDbWriter.cs | 2 +- .../ProteinXmlEntry.cs | 2 +- .../PtmListLoader.cs | 2 +- .../UsefulProteomicsDatabases/UnimodLoader.cs | 2 +- 85 files changed, 163 insertions(+), 160 deletions(-) diff --git a/mzLib/FlashLFQ/FlashLfqEngine.cs b/mzLib/FlashLFQ/FlashLfqEngine.cs index 24617130a..6037e2098 100644 --- a/mzLib/FlashLFQ/FlashLfqEngine.cs +++ b/mzLib/FlashLFQ/FlashLfqEngine.cs @@ -285,7 +285,7 @@ private void CalculateTheoreticalIsotopeDistributions() double massDiff = id.MonoisotopicMass; if (!String.IsNullOrEmpty(id.BaseSequence)) { - MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide baseSequence = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(id.BaseSequence); + Proteomics.AminoAcidPolymer.Peptide baseSequence = new Proteomics.AminoAcidPolymer.Peptide(id.BaseSequence); formula = baseSequence.GetChemicalFormula(); // add averagine for any unknown mass difference (i.e., a modification) massDiff -= baseSequence.MonoisotopicMass; diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/SpectralDeconvolutionAlgorithm.cs b/mzLib/MassSpectrometry/Deconvolution/Algorithms/SpectralDeconvolutionAlgorithm.cs index 7c71d72d9..3470971f0 100644 --- a/mzLib/MassSpectrometry/Deconvolution/Algorithms/SpectralDeconvolutionAlgorithm.cs +++ b/mzLib/MassSpectrometry/Deconvolution/Algorithms/SpectralDeconvolutionAlgorithm.cs @@ -7,8 +7,8 @@ using Easy.Common.Extensions; using MassSpectrometry.Deconvolution; using MassSpectrometry.Deconvolution.Scoring; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.ProteolyticDigestion; using MzLibUtil; namespace MassSpectrometry.Deconvolution.Algorithms diff --git a/mzLib/MassSpectrometry/Deconvolution/Parameters/SpectralDeconvolutionParameters.cs b/mzLib/MassSpectrometry/Deconvolution/Parameters/SpectralDeconvolutionParameters.cs index ffa56e3d6..7e06c032c 100644 --- a/mzLib/MassSpectrometry/Deconvolution/Parameters/SpectralDeconvolutionParameters.cs +++ b/mzLib/MassSpectrometry/Deconvolution/Parameters/SpectralDeconvolutionParameters.cs @@ -3,8 +3,8 @@ using System.Linq; using System.Text; using System.Threading.Tasks; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.ProteolyticDigestion; using MathNet.Numerics.Optimization; using MzLibUtil; diff --git a/mzLib/MassSpectrometry/MzSpectra/IsotopicEnvelope.cs b/mzLib/MassSpectrometry/MzSpectra/IsotopicEnvelope.cs index 78040cf5d..cb9897791 100644 --- a/mzLib/MassSpectrometry/MzSpectra/IsotopicEnvelope.cs +++ b/mzLib/MassSpectrometry/MzSpectra/IsotopicEnvelope.cs @@ -4,7 +4,7 @@ using System.Linq; using Chemistry; using MassSpectrometry.Deconvolution; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics.ProteolyticDigestion; namespace MassSpectrometry { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs index e40d135b4..8c6575ae1 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs @@ -25,7 +25,7 @@ using Chemistry; using MzLibUtil; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { /// /// A linear polymer of amino acids diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymerExtensions.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymerExtensions.cs index d18b3d4c2..2bc13a1f0 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymerExtensions.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/AminoAcidPolymerExtensions.cs @@ -20,7 +20,7 @@ using System.Collections.Generic; using System.Linq; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public static class AminoAcidPolymerExtensions { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaFragment.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaFragment.cs index e025228d0..655b73608 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaFragment.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaFragment.cs @@ -18,7 +18,7 @@ using Chemistry; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class ChemicalFormulaFragment : Fragment, IHasChemicalFormula { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaModification.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaModification.cs index 9a920e256..7f4f93580 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaModification.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaModification.cs @@ -18,7 +18,7 @@ using Chemistry; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class OldSchoolChemicalFormulaModification : OldSchoolModification, IHasChemicalFormula { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaTerminus.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaTerminus.cs index 49e8572ea..3479a5068 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaTerminus.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ChemicalFormulaTerminus.cs @@ -17,7 +17,7 @@ using Chemistry; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class ChemicalFormulaTerminus : IHasChemicalFormula { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/DigestionPoint.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/DigestionPoint.cs index 23a4bac7f..d906b736a 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/DigestionPoint.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/DigestionPoint.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class DigestionPointAndLength { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Fragment.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Fragment.cs index 13c67b5a2..6d0c7806a 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Fragment.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Fragment.cs @@ -21,7 +21,7 @@ using System.Globalization; using Chemistry; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class Fragment : IHasMass, IEquatable { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/FragmentTypes.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/FragmentTypes.cs index 122c37996..5ef1f3c88 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/FragmentTypes.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/FragmentTypes.cs @@ -21,7 +21,7 @@ using Chemistry; using MzLibUtil; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { [Flags] public enum FragmentTypes diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/IProtease.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/IProtease.cs index 76ed17819..60a27219c 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/IProtease.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/IProtease.cs @@ -18,7 +18,7 @@ using System.Collections.Generic; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { /// /// A proteolyic enzyme that cuts amino acids at specific residues. diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationCollection.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationCollection.cs index a4ffd8aed..cb7939c39 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationCollection.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationCollection.cs @@ -24,7 +24,7 @@ using Chemistry; using MzLibUtil; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class ModificationCollection : ICollection, IEquatable, IHasChemicalFormula { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationSites.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationSites.cs index 5115ebac6..e68c7e143 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationSites.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/ModificationSites.cs @@ -19,7 +19,7 @@ using System; using System.Collections.Generic; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { [Flags] public enum ModificationSites diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModification.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModification.cs index 25685362f..2753fbe02 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModification.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModification.cs @@ -20,7 +20,7 @@ using System.Globalization; using Chemistry; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { /// /// Represents a modification with a mass and name and default amino acid sites of modification diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModificationWithMultiplePossibilities.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModificationWithMultiplePossibilities.cs index 82fa9853a..d1039281e 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModificationWithMultiplePossibilities.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/OldSchoolModificationWithMultiplePossibilities.cs @@ -20,7 +20,7 @@ using System.Collections.Generic; using MzLibUtil; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class ModificationWithMultiplePossibilitiesCollection : OldSchoolModification, IEnumerable { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Peptide.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Peptide.cs index 1c3132f9f..4ea4346e6 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Peptide.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Peptide.cs @@ -19,7 +19,7 @@ using System.Collections.Generic; using System.Linq; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class Peptide : AminoAcidPolymer { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Residue.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Residue.cs index 7b797b2cd..4797bec7a 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Residue.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Residue.cs @@ -19,7 +19,7 @@ using System.Collections.Generic; using Chemistry; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { public class Residue : IHasChemicalFormula { diff --git a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Terminus.cs b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Terminus.cs index 159b0612e..0785e835a 100644 --- a/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Terminus.cs +++ b/mzLib/MassSpectrometry/Proteomics/AminoAcidPolymer/Terminus.cs @@ -18,7 +18,7 @@ using System; -namespace MassSpectrometry.Proteomics.AminoAcidPolymer +namespace Proteomics.AminoAcidPolymer { /// /// The terminus of an amino acid polymer N-[Amino Acids]-C diff --git a/mzLib/MassSpectrometry/Proteomics/Fragmentation/DissociationTypeCollection.cs b/mzLib/MassSpectrometry/Proteomics/Fragmentation/DissociationTypeCollection.cs index 105161334..98293c4d9 100644 --- a/mzLib/MassSpectrometry/Proteomics/Fragmentation/DissociationTypeCollection.cs +++ b/mzLib/MassSpectrometry/Proteomics/Fragmentation/DissociationTypeCollection.cs @@ -1,8 +1,9 @@ using System.Collections.Generic; using System.Linq; using Chemistry; +using MassSpectrometry; -namespace MassSpectrometry.Proteomics.Fragmentation +namespace Proteomics.Fragmentation { public class DissociationTypeCollection { diff --git a/mzLib/MassSpectrometry/Proteomics/Fragmentation/FragmentationTerminus.cs b/mzLib/MassSpectrometry/Proteomics/Fragmentation/FragmentationTerminus.cs index a60884bdd..84e8958f8 100644 --- a/mzLib/MassSpectrometry/Proteomics/Fragmentation/FragmentationTerminus.cs +++ b/mzLib/MassSpectrometry/Proteomics/Fragmentation/FragmentationTerminus.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics.Fragmentation +namespace Proteomics.Fragmentation { public enum FragmentationTerminus { diff --git a/mzLib/MassSpectrometry/Proteomics/Fragmentation/MatchedFragmentIon.cs b/mzLib/MassSpectrometry/Proteomics/Fragmentation/MatchedFragmentIon.cs index 834bf0fe7..0f8ade525 100644 --- a/mzLib/MassSpectrometry/Proteomics/Fragmentation/MatchedFragmentIon.cs +++ b/mzLib/MassSpectrometry/Proteomics/Fragmentation/MatchedFragmentIon.cs @@ -1,7 +1,7 @@ using System.Text; using Chemistry; -namespace MassSpectrometry.Proteomics.Fragmentation +namespace Proteomics.Fragmentation { public class MatchedFragmentIon { diff --git a/mzLib/MassSpectrometry/Proteomics/Fragmentation/Product.cs b/mzLib/MassSpectrometry/Proteomics/Fragmentation/Product.cs index 978740540..f8de52f04 100644 --- a/mzLib/MassSpectrometry/Proteomics/Fragmentation/Product.cs +++ b/mzLib/MassSpectrometry/Proteomics/Fragmentation/Product.cs @@ -1,6 +1,6 @@ using System.Text; -namespace MassSpectrometry.Proteomics.Fragmentation +namespace Proteomics.Fragmentation { public struct Product { diff --git a/mzLib/MassSpectrometry/Proteomics/Fragmentation/ProductType.cs b/mzLib/MassSpectrometry/Proteomics/Fragmentation/ProductType.cs index 12bac3e78..10e9bcbab 100644 --- a/mzLib/MassSpectrometry/Proteomics/Fragmentation/ProductType.cs +++ b/mzLib/MassSpectrometry/Proteomics/Fragmentation/ProductType.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics.Fragmentation +namespace Proteomics.Fragmentation { public enum ProductType { diff --git a/mzLib/MassSpectrometry/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs b/mzLib/MassSpectrometry/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs index d8a55add9..543ef482f 100644 --- a/mzLib/MassSpectrometry/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs +++ b/mzLib/MassSpectrometry/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs @@ -1,6 +1,6 @@ using System.Collections.Generic; -namespace MassSpectrometry.Proteomics.Fragmentation +namespace Proteomics.Fragmentation { public class TerminusSpecificProductTypes { diff --git a/mzLib/MassSpectrometry/Proteomics/Modifications/ModLocationOnPeptideOrProtein.cs b/mzLib/MassSpectrometry/Proteomics/Modifications/ModLocationOnPeptideOrProtein.cs index a52aa5987..4a143a3fa 100644 --- a/mzLib/MassSpectrometry/Proteomics/Modifications/ModLocationOnPeptideOrProtein.cs +++ b/mzLib/MassSpectrometry/Proteomics/Modifications/ModLocationOnPeptideOrProtein.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics +namespace Proteomics { public enum ModLocationOnPeptideOrProtein { diff --git a/mzLib/MassSpectrometry/Proteomics/Modifications/Modification.cs b/mzLib/MassSpectrometry/Proteomics/Modifications/Modification.cs index d0a5c24dc..711aaf32b 100644 --- a/mzLib/MassSpectrometry/Proteomics/Modifications/Modification.cs +++ b/mzLib/MassSpectrometry/Proteomics/Modifications/Modification.cs @@ -3,8 +3,9 @@ using System.Linq; using System.Text; using Chemistry; +using MassSpectrometry; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class Modification { diff --git a/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationLocalization.cs b/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationLocalization.cs index 6a8cd39a2..b12c0e19c 100644 --- a/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationLocalization.cs +++ b/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationLocalization.cs @@ -2,7 +2,7 @@ using System.Collections.Generic; using System.Linq; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public static class ModificationLocalization { diff --git a/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationMotif.cs b/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationMotif.cs index 163994f57..204ed16a4 100644 --- a/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationMotif.cs +++ b/mzLib/MassSpectrometry/Proteomics/Modifications/ModificationMotif.cs @@ -1,7 +1,7 @@ using System.Linq; using System.Text.RegularExpressions; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class ModificationMotif { diff --git a/mzLib/MassSpectrometry/Proteomics/Modifications/SilacLabel.cs b/mzLib/MassSpectrometry/Proteomics/Modifications/SilacLabel.cs index a978cc8e7..d6376a3f7 100644 --- a/mzLib/MassSpectrometry/Proteomics/Modifications/SilacLabel.cs +++ b/mzLib/MassSpectrometry/Proteomics/Modifications/SilacLabel.cs @@ -2,7 +2,7 @@ using System.Collections.Generic; using System.Globalization; -namespace MassSpectrometry.Proteomics +namespace Proteomics { /// /// Silac labels used to modify unlabeled proteins diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/DatabaseReference.cs b/mzLib/MassSpectrometry/Proteomics/Protein/DatabaseReference.cs index 85cab7e65..b9945a142 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/DatabaseReference.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/DatabaseReference.cs @@ -2,7 +2,7 @@ using System.Collections.Generic; using System.Linq; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class DatabaseReference { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/DisulfideBond.cs b/mzLib/MassSpectrometry/Proteomics/Protein/DisulfideBond.cs index 9167706b0..6bd4fa1af 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/DisulfideBond.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/DisulfideBond.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class DisulfideBond { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/Protein.cs b/mzLib/MassSpectrometry/Proteomics/Protein/Protein.cs index 50079e525..7ec98d9e4 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/Protein.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/Protein.cs @@ -2,11 +2,11 @@ using System.Collections.Generic; using System.Linq; using System.Text.RegularExpressions; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics.Fragmentation; +using Proteomics; +using Proteomics.ProteolyticDigestion; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class Protein { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/ProteoformLevelClassifier.cs b/mzLib/MassSpectrometry/Proteomics/Protein/ProteoformLevelClassifier.cs index c143a8664..e89956e8c 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/ProteoformLevelClassifier.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/ProteoformLevelClassifier.cs @@ -2,9 +2,9 @@ using System.Collections.Generic; using System.Linq; using System.Text; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics.ProteolyticDigestion; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public static class ProteoformLevelClassifier { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/ProteolysisProduct.cs b/mzLib/MassSpectrometry/Proteomics/Protein/ProteolysisProduct.cs index 45aef97bf..81eaebdc3 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/ProteolysisProduct.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/ProteolysisProduct.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class ProteolysisProduct { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariantDescription.cs b/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariantDescription.cs index 51e9ecadb..d19493dd8 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariantDescription.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariantDescription.cs @@ -2,7 +2,7 @@ using System.Collections.Generic; using System.Linq; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class SequenceVariantDescription { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariation.cs b/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariation.cs index ad807219e..84642db46 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariation.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/SequenceVariation.cs @@ -1,8 +1,8 @@ using System.Collections.Generic; using System.Linq; -using MassSpectrometry.Proteomics; +using Proteomics; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class SequenceVariation { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/SnpEffAnnotation.cs b/mzLib/MassSpectrometry/Proteomics/Protein/SnpEffAnnotation.cs index 67a72f77b..62330a9c3 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/SnpEffAnnotation.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/SnpEffAnnotation.cs @@ -2,7 +2,7 @@ using System.Linq; using System.Text.RegularExpressions; -namespace MassSpectrometry.Proteomics +namespace Proteomics { /// /// Specifications are described here: http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/SpliceSite.cs b/mzLib/MassSpectrometry/Proteomics/Protein/SpliceSite.cs index 044d4bf30..c1c7cfadb 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/SpliceSite.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/SpliceSite.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics +namespace Proteomics { public class SpliceSite { diff --git a/mzLib/MassSpectrometry/Proteomics/Protein/VariantApplication.cs b/mzLib/MassSpectrometry/Proteomics/Protein/VariantApplication.cs index f5c0ee363..f2554694e 100644 --- a/mzLib/MassSpectrometry/Proteomics/Protein/VariantApplication.cs +++ b/mzLib/MassSpectrometry/Proteomics/Protein/VariantApplication.cs @@ -1,9 +1,9 @@ using System; using System.Collections.Generic; using System.Linq; -using MassSpectrometry.Proteomics; +using Proteomics; -namespace MassSpectrometry.Proteomics +namespace Proteomics { public static class VariantApplication { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/CleavageSpecificity.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/CleavageSpecificity.cs index e346df738..c09f06ebd 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/CleavageSpecificity.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/CleavageSpecificity.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public enum CleavageSpecificity { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionMotif.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionMotif.cs index a92814504..d4cc67c12 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionMotif.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionMotif.cs @@ -3,7 +3,7 @@ using System.Text.RegularExpressions; using MzLibUtil; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public class DigestionMotif { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionParams.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionParams.cs index edd1f4c8f..612e5a77c 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionParams.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/DigestionParams.cs @@ -1,6 +1,6 @@ -using MassSpectrometry.Proteomics.Fragmentation; +using Proteomics.Fragmentation; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public class DigestionParams { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/InitiatorMethionineBehavior.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/InitiatorMethionineBehavior.cs index 582e32a4b..2df741374 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/InitiatorMethionineBehavior.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/InitiatorMethionineBehavior.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public enum InitiatorMethionineBehavior { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs index 867fb9a54..3cc15bb0a 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs @@ -3,10 +3,11 @@ using System.Linq; using System.Text; using Chemistry; -using MassSpectrometry.Proteomics.AminoAcidPolymer; -using MassSpectrometry.Proteomics.Fragmentation; +using Proteomics.AminoAcidPolymer; +using Proteomics.Fragmentation; +using MassSpectrometry; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { [Serializable] public class PeptideWithSetModifications : ProteolyticPeptide diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProductTypeMethods.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProductTypeMethods.cs index 94961983d..2606ce068 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProductTypeMethods.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProductTypeMethods.cs @@ -1,8 +1,8 @@ using System; using System.Collections.Generic; -using MassSpectrometry.Proteomics.Fragmentation; +using Proteomics.Fragmentation; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public static class ProductTypeMethods { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/Protease.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/Protease.cs index dffb29a73..93b649cbe 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/Protease.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/Protease.cs @@ -1,9 +1,9 @@ using System; using System.Collections.Generic; using System.Linq; -using MassSpectrometry.Proteomics; +using Proteomics; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public class Protease { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteaseDictionary.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteaseDictionary.cs index 33fa9dcfe..a667653a8 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteaseDictionary.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteaseDictionary.cs @@ -3,9 +3,9 @@ using System.IO; using System.Linq; using MzLibUtil; -using MassSpectrometry.Proteomics; +using Proteomics; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public static class ProteaseDictionary { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteinDigestion.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteinDigestion.cs index 7e7d0ed8b..cf5d9ce0b 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteinDigestion.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteinDigestion.cs @@ -1,7 +1,7 @@ using System.Collections.Generic; -using MassSpectrometry.Proteomics.Fragmentation; +using Proteomics.Fragmentation; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { public class ProteinDigestion { diff --git a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs index e484f3b81..4ef3f5150 100644 --- a/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs +++ b/mzLib/MassSpectrometry/Proteomics/ProteolyticDigestion/ProteolyticPeptide.cs @@ -1,9 +1,9 @@ using System; using System.Collections.Generic; using System.Linq; -using MassSpectrometry.Proteomics; +using Proteomics; -namespace MassSpectrometry.Proteomics.ProteolyticDigestion +namespace Proteomics.ProteolyticDigestion { /// /// Product of digesting a protein diff --git a/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/CZE.cs b/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/CZE.cs index f98b51261..846291ced 100644 --- a/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/CZE.cs +++ b/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/CZE.cs @@ -1,6 +1,6 @@ using System; -namespace MassSpectrometry.Proteomics.RetentionTimePrediction +namespace Proteomics.RetentionTimePrediction { /// /// This class will return theoretical retention times, hydrobphobicites, electrophoretic mobilities and etc. for peptides. diff --git a/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SSRCalc3.cs b/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SSRCalc3.cs index 90a9838bb..92734045a 100644 --- a/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SSRCalc3.cs +++ b/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SSRCalc3.cs @@ -3,9 +3,9 @@ using System.Linq; using System.Text; using System.Text.RegularExpressions; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics.ProteolyticDigestion; -namespace MassSpectrometry.Proteomics.RetentionTimePrediction +namespace Proteomics.RetentionTimePrediction { /** /* diff --git a/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SeparationType.cs b/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SeparationType.cs index d33287f2d..abc460533 100644 --- a/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SeparationType.cs +++ b/mzLib/MassSpectrometry/Proteomics/RetentionTimePrediction/SeparationType.cs @@ -1,4 +1,4 @@ -namespace MassSpectrometry.Proteomics.RetentionTimePrediction +namespace Proteomics.RetentionTimePrediction { public enum SeparationType { diff --git a/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs b/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs index 48757ab74..9e62afe60 100644 --- a/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs +++ b/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs @@ -20,7 +20,7 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/DatabaseTests/TestProteinReader.cs b/mzLib/Test/DatabaseTests/TestProteinReader.cs index 0ecefea64..2ea4e589d 100644 --- a/mzLib/Test/DatabaseTests/TestProteinReader.cs +++ b/mzLib/Test/DatabaseTests/TestProteinReader.cs @@ -17,7 +17,7 @@ // License along with MassSpectrometry.Tests. If not, see . using NUnit.Framework; -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs b/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs index cd26cd58b..795e813f7 100644 --- a/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs +++ b/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs @@ -1,8 +1,8 @@ using MassSpectrometry; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.Fragmentation; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/DatabaseTests/TestVariantProtein.cs b/mzLib/Test/DatabaseTests/TestVariantProtein.cs index 33ba6e6ac..cf30c43fa 100644 --- a/mzLib/Test/DatabaseTests/TestVariantProtein.cs +++ b/mzLib/Test/DatabaseTests/TestVariantProtein.cs @@ -1,6 +1,6 @@ using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/TestAminoAcids.cs b/mzLib/Test/TestAminoAcids.cs index 778b40d48..e16eb671a 100644 --- a/mzLib/Test/TestAminoAcids.cs +++ b/mzLib/Test/TestAminoAcids.cs @@ -18,7 +18,7 @@ using Chemistry; using NUnit.Framework; -using MassSpectrometry.Proteomics.AminoAcidPolymer; +using Proteomics.AminoAcidPolymer; using System; using System.Diagnostics.CodeAnalysis; using Stopwatch = System.Diagnostics.Stopwatch; diff --git a/mzLib/Test/TestDeconvolution.cs b/mzLib/Test/TestDeconvolution.cs index 8d2afc708..44a0422f0 100644 --- a/mzLib/Test/TestDeconvolution.cs +++ b/mzLib/Test/TestDeconvolution.cs @@ -3,8 +3,8 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.Diagnostics.CodeAnalysis; diff --git a/mzLib/Test/TestDigestionMotif.cs b/mzLib/Test/TestDigestionMotif.cs index 5b77443b5..c58d9e63b 100644 --- a/mzLib/Test/TestDigestionMotif.cs +++ b/mzLib/Test/TestDigestionMotif.cs @@ -1,7 +1,7 @@ using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.Diagnostics.CodeAnalysis; @@ -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, MassSpectrometry.Proteomics.Fragmentation.FragmentationTerminus.N); - DigestionParams speedySemiC = new DigestionParams("trypsin", 10, 29, 30, 1024, InitiatorMethionineBehavior.Retain, 2, CleavageSpecificity.Semi, MassSpectrometry.Proteomics.Fragmentation.FragmentationTerminus.C); + 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); List pwsmsN = humanInsulin.Digest(speedySemiN, null, null).ToList(); List 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 e31997d20..9bbdfe6ba 100644 --- a/mzLib/Test/TestFragments.cs +++ b/mzLib/Test/TestFragments.cs @@ -21,10 +21,10 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.AminoAcidPolymer; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.AminoAcidPolymer; +using Proteomics.Fragmentation; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.Linq; diff --git a/mzLib/Test/TestIsolation.cs b/mzLib/Test/TestIsolation.cs index e13fc4b9e..73c055ac6 100644 --- a/mzLib/Test/TestIsolation.cs +++ b/mzLib/Test/TestIsolation.cs @@ -19,7 +19,7 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics.AminoAcidPolymer; +using Proteomics.AminoAcidPolymer; using System; using System.Linq; using Stopwatch = System.Diagnostics.Stopwatch; diff --git a/mzLib/Test/TestIsotopicEnvelope.cs b/mzLib/Test/TestIsotopicEnvelope.cs index 69844ca78..10f8fb192 100644 --- a/mzLib/Test/TestIsotopicEnvelope.cs +++ b/mzLib/Test/TestIsotopicEnvelope.cs @@ -5,8 +5,8 @@ using System.Threading.Tasks; using Chemistry; using MassSpectrometry; -using MassSpectrometry.Proteomics.ProteolyticDigestion; -using MassSpectrometry.Proteomics; +using Proteomics.ProteolyticDigestion; +using Proteomics; using NUnit.Framework; namespace Test diff --git a/mzLib/Test/TestModFits.cs b/mzLib/Test/TestModFits.cs index cf354faa3..3360bb7a3 100644 --- a/mzLib/Test/TestModFits.cs +++ b/mzLib/Test/TestModFits.cs @@ -1,5 +1,5 @@ using NUnit.Framework; -using MassSpectrometry.Proteomics; +using Proteomics; using System; using Stopwatch = System.Diagnostics.Stopwatch; diff --git a/mzLib/Test/TestModifications.cs b/mzLib/Test/TestModifications.cs index 95716a523..725da2931 100644 --- a/mzLib/Test/TestModifications.cs +++ b/mzLib/Test/TestModifications.cs @@ -20,10 +20,10 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.AminoAcidPolymer; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.AminoAcidPolymer; +using Proteomics.Fragmentation; +using Proteomics.ProteolyticDigestion; using System; using System.Collections; using System.Collections.Generic; diff --git a/mzLib/Test/TestMsDataFile.cs b/mzLib/Test/TestMsDataFile.cs index 5e15acdd3..811935431 100644 --- a/mzLib/Test/TestMsDataFile.cs +++ b/mzLib/Test/TestMsDataFile.cs @@ -21,9 +21,9 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.AminoAcidPolymer; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.AminoAcidPolymer; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/TestMzML.cs b/mzLib/Test/TestMzML.cs index ac36ee851..45eebffc9 100644 --- a/mzLib/Test/TestMzML.cs +++ b/mzLib/Test/TestMzML.cs @@ -4,7 +4,7 @@ using MzIdentML; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics.AminoAcidPolymer; +using Proteomics.AminoAcidPolymer; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/TestPeptideWithSetMods.cs b/mzLib/Test/TestPeptideWithSetMods.cs index dea185cc2..b97729050 100644 --- a/mzLib/Test/TestPeptideWithSetMods.cs +++ b/mzLib/Test/TestPeptideWithSetMods.cs @@ -1,8 +1,8 @@ using Chemistry; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.Fragmentation; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/TestPeptides.cs b/mzLib/Test/TestPeptides.cs index b9faf0493..80cff0f71 100644 --- a/mzLib/Test/TestPeptides.cs +++ b/mzLib/Test/TestPeptides.cs @@ -19,9 +19,9 @@ using Chemistry; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics.AminoAcidPolymer; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics.AminoAcidPolymer; +using Proteomics.Fragmentation; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.Linq; diff --git a/mzLib/Test/TestProductMassesMightHaveDuplicates.cs b/mzLib/Test/TestProductMassesMightHaveDuplicates.cs index dc7a906c8..18dc5b6f0 100644 --- a/mzLib/Test/TestProductMassesMightHaveDuplicates.cs +++ b/mzLib/Test/TestProductMassesMightHaveDuplicates.cs @@ -1,9 +1,9 @@ using Chemistry; using MassSpectrometry; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.Fragmentation; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.Linq; diff --git a/mzLib/Test/TestProteinDatabase.cs b/mzLib/Test/TestProteinDatabase.cs index 8c97c8bc6..f3261c1ac 100644 --- a/mzLib/Test/TestProteinDatabase.cs +++ b/mzLib/Test/TestProteinDatabase.cs @@ -1,5 +1,5 @@ using NUnit.Framework; -using MassSpectrometry.Proteomics; +using Proteomics; using System.Collections.Generic; using System.IO; using System.Linq; diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index 41f7fff32..d808588bb 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -1,10 +1,10 @@ using Chemistry; using MassSpectrometry; using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.AminoAcidPolymer; -using MassSpectrometry.Proteomics.Fragmentation; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.AminoAcidPolymer; +using Proteomics.Fragmentation; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/TestProteinProperties.cs b/mzLib/Test/TestProteinProperties.cs index c468551fb..929c08eca 100644 --- a/mzLib/Test/TestProteinProperties.cs +++ b/mzLib/Test/TestProteinProperties.cs @@ -1,5 +1,5 @@ using NUnit.Framework; -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/TestPtmListLoader.cs b/mzLib/Test/TestPtmListLoader.cs index ab57ef22c..d70946717 100644 --- a/mzLib/Test/TestPtmListLoader.cs +++ b/mzLib/Test/TestPtmListLoader.cs @@ -1,6 +1,6 @@ using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.IO; using System.Linq; diff --git a/mzLib/Test/TestRetentionTimePrediction.cs b/mzLib/Test/TestRetentionTimePrediction.cs index c42bc3d1f..fb197279d 100644 --- a/mzLib/Test/TestRetentionTimePrediction.cs +++ b/mzLib/Test/TestRetentionTimePrediction.cs @@ -1,7 +1,7 @@ using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; -using MassSpectrometry.Proteomics.RetentionTimePrediction; +using Proteomics; +using Proteomics.ProteolyticDigestion; +using Proteomics.RetentionTimePrediction; using System; using System.Collections.Generic; using Stopwatch = System.Diagnostics.Stopwatch; diff --git a/mzLib/Test/TestSeqCoverage.cs b/mzLib/Test/TestSeqCoverage.cs index 3db1ec0ff..f7ce51e85 100644 --- a/mzLib/Test/TestSeqCoverage.cs +++ b/mzLib/Test/TestSeqCoverage.cs @@ -1,6 +1,6 @@ using NUnit.Framework; -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.ProteolyticDigestion; +using Proteomics; +using Proteomics.ProteolyticDigestion; using System; using System.Collections.Generic; using System.IO; diff --git a/mzLib/TestFlashLFQ/TestFlashLFQ.cs b/mzLib/TestFlashLFQ/TestFlashLFQ.cs index 88f761f4a..1554e7dbc 100644 --- a/mzLib/TestFlashLFQ/TestFlashLFQ.cs +++ b/mzLib/TestFlashLFQ/TestFlashLFQ.cs @@ -5,7 +5,7 @@ using MathNet.Numerics.Statistics; using MzLibUtil; using NUnit.Framework; -using MassSpectrometry.Proteomics.AminoAcidPolymer; +using Proteomics.AminoAcidPolymer; using System; using System.Collections.Generic; using System.IO; @@ -316,7 +316,7 @@ public static void TestFlashLfqMatchBetweenRuns() for (int p = 0; p < pepSequences.Count; p++) { - ChemicalFormula cf = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(pepSequences[p]).GetChemicalFormula(); + ChemicalFormula cf = new Proteomics.AminoAcidPolymer.Peptide(pepSequences[p]).GetChemicalFormula(); IsotopicDistribution dist = IsotopicDistribution.GetDistribution(cf, 0.125, 1e-8); double[] mz = dist.Masses.Select(v => v.ToMz(1)).ToArray(); double[] intensities = dist.Intensities.Select(v => v * intensity).ToArray(); @@ -348,25 +348,25 @@ public static void TestFlashLfqMatchBetweenRuns() // create some PSMs var pg = new ProteinGroup("MyProtein", "gene", "org"); Identification id1 = new Identification(file1, "PEPTIDE", "PEPTIDE", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDE").MonoisotopicMass, file1Rt[0] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDE").MonoisotopicMass, file1Rt[0] + 0.001, 1, new List { pg }); Identification id2 = new Identification(file1, "PEPTIDEV", "PEPTIDEV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEV").MonoisotopicMass, file1Rt[1] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEV").MonoisotopicMass, file1Rt[1] + 0.001, 1, new List { pg }); Identification id3 = new Identification(file1, "PEPTIDEVV", "PEPTIDEVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVV").MonoisotopicMass, file1Rt[2] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVV").MonoisotopicMass, file1Rt[2] + 0.001, 1, new List { pg }); Identification id4 = new Identification(file1, "PEPTIDEVVV", "PEPTIDEVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVV").MonoisotopicMass, file1Rt[3] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVV").MonoisotopicMass, file1Rt[3] + 0.001, 1, new List { pg }); Identification id5 = new Identification(file1, "PEPTIDEVVVV", "PEPTIDEVVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVVV").MonoisotopicMass, file1Rt[4] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVVV").MonoisotopicMass, file1Rt[4] + 0.001, 1, new List { pg }); Identification id6 = new Identification(file2, "PEPTIDE", "PEPTIDE", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDE").MonoisotopicMass, file2Rt[0] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDE").MonoisotopicMass, file2Rt[0] + 0.001, 1, new List { pg }); Identification id7 = new Identification(file2, "PEPTIDEV", "PEPTIDEV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEV").MonoisotopicMass, file2Rt[1] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEV").MonoisotopicMass, file2Rt[1] + 0.001, 1, new List { pg }); // missing ID 8 - MBR feature Identification id9 = new Identification(file2, "PEPTIDEVVV", "PEPTIDEVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVV").MonoisotopicMass, file2Rt[3] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVV").MonoisotopicMass, file2Rt[3] + 0.001, 1, new List { pg }); Identification id10 = new Identification(file2, "PEPTIDEVVVV", "PEPTIDEVVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVVV").MonoisotopicMass, file2Rt[4] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVVV").MonoisotopicMass, file2Rt[4] + 0.001, 1, new List { pg }); // create the FlashLFQ engine FlashLfqEngine engine = new FlashLfqEngine(new List { id1, id2, id3, id4, id5, id6, id7, id9, id10 }, matchBetweenRuns: true); @@ -408,7 +408,7 @@ public static void TestPeakSplittingLeft() for (int s = 0; s < scans.Length; s++) { - ChemicalFormula cf = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); + ChemicalFormula cf = new Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); IsotopicDistribution dist = IsotopicDistribution.GetDistribution(cf, 0.125, 1e-8); double[] mz = dist.Masses.Select(v => v.ToMz(1)).ToArray(); double[] intensities = dist.Intensities.Select(v => v * intensity * intensityMultipliers[s]).ToArray(); @@ -430,7 +430,7 @@ public static void TestPeakSplittingLeft() var pg = new ProteinGroup("MyProtein", "gene", "org"); Identification id1 = new Identification(file1, peptide, peptide, - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.7 + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.7 + 0.001, 1, new List { pg }); // create the FlashLFQ engine FlashLfqEngine engine = new FlashLfqEngine(new List { id1 }); @@ -462,7 +462,7 @@ public static void TestPeakSplittingRight() for (int s = 0; s < scans.Length; s++) { - ChemicalFormula cf = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); + ChemicalFormula cf = new Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); IsotopicDistribution dist = IsotopicDistribution.GetDistribution(cf, 0.125, 1e-8); double[] mz = dist.Masses.Select(v => v.ToMz(1)).ToArray(); double[] intensities = dist.Intensities.Select(v => v * intensity * intensityMultipliers[s]).ToArray(); @@ -484,7 +484,7 @@ public static void TestPeakSplittingRight() var pg = new ProteinGroup("MyProtein", "gene", "org"); Identification id1 = new Identification(file1, peptide, peptide, - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.3 + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.3 + 0.001, 1, new List { pg }); // create the FlashLFQ engine FlashLfqEngine engine = new FlashLfqEngine(new List { id1 }); @@ -516,7 +516,7 @@ public static void TestPeakSplittingRightWithEmptyScan() for (int s = 0; s < scans.Length; s++) { - ChemicalFormula cf = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); + ChemicalFormula cf = new Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); IsotopicDistribution dist = IsotopicDistribution.GetDistribution(cf, 0.125, 1e-8); double[] mz = dist.Masses.Select(v => v.ToMz(1)).ToArray(); double[] intensities = dist.Intensities.Select(v => v * intensity * intensityMultipliers[s]).ToArray(); @@ -544,7 +544,7 @@ public static void TestPeakSplittingRightWithEmptyScan() var pg = new ProteinGroup("MyProtein", "gene", "org"); Identification id1 = new Identification(file1, peptide, peptide, - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.3 + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.3 + 0.001, 1, new List { pg }); // create the FlashLFQ engine FlashLfqEngine engine = new FlashLfqEngine(new List { id1 }); @@ -576,7 +576,7 @@ public static void TestPeakSplittingLeftWithEmptyScan() for (int s = 0; s < scans.Length; s++) { - ChemicalFormula cf = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); + ChemicalFormula cf = new Proteomics.AminoAcidPolymer.Peptide(peptide).GetChemicalFormula(); IsotopicDistribution dist = IsotopicDistribution.GetDistribution(cf, 0.125, 1e-8); double[] mz = dist.Masses.Select(v => v.ToMz(1)).ToArray(); double[] intensities = dist.Intensities.Select(v => v * intensity * intensityMultipliers[s]).ToArray(); @@ -604,7 +604,7 @@ public static void TestPeakSplittingLeftWithEmptyScan() var pg = new ProteinGroup("MyProtein", "gene", "org"); Identification id1 = new Identification(file1, peptide, peptide, - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.3 + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide(peptide).MonoisotopicMass, 1.3 + 0.001, 1, new List { pg }); // create the FlashLFQ engine FlashLfqEngine engine = new FlashLfqEngine(new List { id1 }); @@ -716,7 +716,7 @@ public static void TestMatchBetweenRunsWithNoIdsInCommon() for (int p = 0; p < pepSequences.Count; p++) { - ChemicalFormula cf = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(pepSequences[p]).GetChemicalFormula(); + ChemicalFormula cf = new Proteomics.AminoAcidPolymer.Peptide(pepSequences[p]).GetChemicalFormula(); IsotopicDistribution dist = IsotopicDistribution.GetDistribution(cf, 0.125, 1e-8); double[] mz = dist.Masses.Select(v => v.ToMz(1)).ToArray(); double[] intensities = dist.Intensities.Select(v => v * intensity).ToArray(); @@ -750,25 +750,25 @@ public static void TestMatchBetweenRunsWithNoIdsInCommon() var myMbrProteinGroup = new ProteinGroup("MyMbrProtein", "MbrGene", "org"); Identification id1 = new Identification(file1, "PEPTIDE", "PEPTIDE", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDE").MonoisotopicMass, file1Rt[0] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDE").MonoisotopicMass, file1Rt[0] + 0.001, 1, new List { pg }); Identification id2 = new Identification(file1, "PEPTIDEV", "PEPTIDEV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEV").MonoisotopicMass, file1Rt[1] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEV").MonoisotopicMass, file1Rt[1] + 0.001, 1, new List { pg }); Identification id3 = new Identification(file1, "PEPTIDEVV", "PEPTIDEVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVV").MonoisotopicMass, file1Rt[2] + 0.001, 1, new List { myMbrProteinGroup }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVV").MonoisotopicMass, file1Rt[2] + 0.001, 1, new List { myMbrProteinGroup }); Identification id4 = new Identification(file1, "PEPTIDEVVV", "PEPTIDEVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVV").MonoisotopicMass, file1Rt[3] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVV").MonoisotopicMass, file1Rt[3] + 0.001, 1, new List { pg }); Identification id5 = new Identification(file1, "PEPTIDEVVVV", "PEPTIDEVVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVVV").MonoisotopicMass, file1Rt[4] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIDEVVVV").MonoisotopicMass, file1Rt[4] + 0.001, 1, new List { pg }); Identification id6 = new Identification(file2, "PEPTIED", "PEPTIED", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIED").MonoisotopicMass, file2Rt[0] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIED").MonoisotopicMass, file2Rt[0] + 0.001, 1, new List { pg }); Identification id7 = new Identification(file2, "PEPTIEDV", "PEPTIEDV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIEDV").MonoisotopicMass, file2Rt[1] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIEDV").MonoisotopicMass, file2Rt[1] + 0.001, 1, new List { pg }); // missing ID 8 - MBR feature Identification id9 = new Identification(file2, "PEPTIEDVVV", "PEPTIEDVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIEDVVV").MonoisotopicMass, file2Rt[3] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIEDVVV").MonoisotopicMass, file2Rt[3] + 0.001, 1, new List { pg }); Identification id10 = new Identification(file2, "PEPTIEDVVVV", "PEPTIEDVVVV", - new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide("PEPTIEDVVVV").MonoisotopicMass, file2Rt[4] + 0.001, 1, new List { pg }); + new Proteomics.AminoAcidPolymer.Peptide("PEPTIEDVVVV").MonoisotopicMass, file2Rt[4] + 0.001, 1, new List { pg }); FlashLfqEngine engine = new FlashLfqEngine(new List { id1, id2, id3, id4, id5, id6, id7, id9, id10 }, matchBetweenRuns: true); var results = engine.Run(); @@ -1021,7 +1021,7 @@ public static void ProteoformPeakfindingTest() MsDataScan[] scans = new MsDataScan[10]; - ChemicalFormula cf = new MassSpectrometry.Proteomics.AminoAcidPolymer.Peptide(sequence).GetChemicalFormula(); + ChemicalFormula cf = new Proteomics.AminoAcidPolymer.Peptide(sequence).GetChemicalFormula(); IsotopicDistribution dist = IsotopicDistribution.GetDistribution(cf, 0.125, 1e-8); double[] mz = dist.Masses.Select(v => v.ToMz(charge)).ToArray(); diff --git a/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs b/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs index 1621e4abc..4da442aee 100644 --- a/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs +++ b/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs @@ -1,4 +1,4 @@ -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.Linq; diff --git a/mzLib/UsefulProteomicsDatabases/Loaders.cs b/mzLib/UsefulProteomicsDatabases/Loaders.cs index 2a77faea3..a64792da2 100644 --- a/mzLib/UsefulProteomicsDatabases/Loaders.cs +++ b/mzLib/UsefulProteomicsDatabases/Loaders.cs @@ -16,7 +16,7 @@ // License along with UsefulProteomicsDatabases. If not, see . using Chemistry; -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.Globalization; diff --git a/mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs b/mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs index 1d6f56cd7..2f4db2ce0 100644 --- a/mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs +++ b/mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs @@ -1,5 +1,5 @@ -using MassSpectrometry.Proteomics; -using MassSpectrometry.Proteomics.AminoAcidPolymer; +using Proteomics; +using Proteomics.AminoAcidPolymer; using System; using System.Collections.Generic; using System.Diagnostics.CodeAnalysis; diff --git a/mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs b/mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs index c3ca39c06..2ca130ed6 100644 --- a/mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs +++ b/mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs @@ -1,4 +1,4 @@ -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.Globalization; diff --git a/mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs b/mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs index 06106903f..95a9ce5ac 100644 --- a/mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs +++ b/mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs @@ -1,4 +1,4 @@ -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.Linq; diff --git a/mzLib/UsefulProteomicsDatabases/PtmListLoader.cs b/mzLib/UsefulProteomicsDatabases/PtmListLoader.cs index 11048ebba..ddcd50268 100644 --- a/mzLib/UsefulProteomicsDatabases/PtmListLoader.cs +++ b/mzLib/UsefulProteomicsDatabases/PtmListLoader.cs @@ -1,7 +1,7 @@ using Chemistry; using MassSpectrometry; using MzLibUtil; -using MassSpectrometry.Proteomics; +using Proteomics; using System; using System.Collections.Generic; using System.Globalization; diff --git a/mzLib/UsefulProteomicsDatabases/UnimodLoader.cs b/mzLib/UsefulProteomicsDatabases/UnimodLoader.cs index ac23ee608..56512e841 100644 --- a/mzLib/UsefulProteomicsDatabases/UnimodLoader.cs +++ b/mzLib/UsefulProteomicsDatabases/UnimodLoader.cs @@ -1,5 +1,5 @@ using Chemistry; -using MassSpectrometry.Proteomics; +using Proteomics; using System.Collections.Generic; using System.IO; using System.Xml.Serialization;