Changed MassSpectrometry.Proteomics* namespace back to Proteomics*

smith-chem-wisc · Dec 12, 2022 · c9174ea · c9174ea
1 parent 1193d17
commit c9174ea
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Showing 85 changed files with 163 additions and 160 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -25,7 +25,7 @@
 using Chemistry;
 using MzLibUtil;
 
-namespace MassSpectrometry.Proteomics.AminoAcidPolymer
+namespace Proteomics.AminoAcidPolymer
 {
     /// <summary>
     /// A linear polymer of amino acids

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -21,7 +21,7 @@
 using System.Globalization;
 using Chemistry;
 
-namespace MassSpectrometry.Proteomics.AminoAcidPolymer
+namespace Proteomics.AminoAcidPolymer
 {
     public class Fragment : IHasMass, IEquatable<Fragment>
     {

diff --git 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
@@ -18,7 +18,7 @@
 
 using System.Collections.Generic;
 
-namespace MassSpectrometry.Proteomics.AminoAcidPolymer
+namespace Proteomics.AminoAcidPolymer
 {
     /// <summary>
     /// 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
@@ -24,7 +24,7 @@
 using Chemistry;
 using MzLibUtil;
 
-namespace MassSpectrometry.Proteomics.AminoAcidPolymer
+namespace Proteomics.AminoAcidPolymer
 {
     public class ModificationCollection : ICollection<IHasMass>, IEquatable<ModificationCollection>, IHasChemicalFormula
     {

diff --git 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
@@ -20,7 +20,7 @@
 using System.Globalization;
 using Chemistry;
 
-namespace MassSpectrometry.Proteomics.AminoAcidPolymer
+namespace Proteomics.AminoAcidPolymer
 {
     /// <summary>
     /// Represents a modification with a mass and name and default amino acid sites of modification

diff --git a/...pectrometry/Proteomics/AminoAcidPolymer/OldSchoolModificationWithMultiplePossibilities.cs b/...pectrometry/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<OldSchoolModification>
     {

diff --git 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
@@ -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
@@ -18,7 +18,7 @@
 
 using System;
 
-namespace MassSpectrometry.Proteomics.AminoAcidPolymer
+namespace Proteomics.AminoAcidPolymer
 {
     /// <summary>
     /// 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -2,7 +2,7 @@
 using System.Collections.Generic;
 using System.Globalization;
 
-namespace MassSpectrometry.Proteomics
+namespace Proteomics
 {
     /// <summary>
     /// Silac labels used to modify unlabeled proteins

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -2,7 +2,7 @@
 using System.Linq;
 using System.Text.RegularExpressions;
 
-namespace MassSpectrometry.Proteomics
+namespace Proteomics
 {
     /// <summary>
     /// 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,4 @@
-namespace MassSpectrometry.Proteomics.ProteolyticDigestion
+namespace Proteomics.ProteolyticDigestion
 {
     public enum InitiatorMethionineBehavior
     {