Major change to how masses are calculated. Remove lazy evalution from…

… Chemical formula and Amino Acid Polymer for significant speed improvements.

.gitignore

@@ -45,6 +45,9 @@ ehthumbs.db
 # TESTS #
 #########
 TestResults/
+*.psess
+*.vsp
+
 
 # Nuget #
 #########

CSMSL.Examples/Examples.cs

@@ -49,14 +49,14 @@ private static void Main(string[] args)
         private static void StartExamples()
         {   
             // Examples coding
-            ChemicalFormulaExamples();
+            //ChemicalFormulaExamples();
             //PeptideExamples();
 
             // Example Objects
             //VennDiagramExamples();
 
             // Example programs
-            //TrypticDigestion.Start(Protease.Trypsin);
+            TrypticDigestion.Start(Protease.Trypsin);
 
             // Example Protein Grouping
             //ProteinGroupingExample.Start(Protease.Trypsin);
@@ -203,19 +203,19 @@ private static void ChemicalFormulaExamples()
         /// <param name="formula"></param>
         private static void WriteFormulaToConsole(ChemicalFormula formula)
         {
-            Console.WriteLine("Formula {0} mass is {1}", formula, formula.Mass.Monoisotopic);
+            Console.WriteLine("Formula {0} mass is {1} or {2}", formula, formula.Mass.MonoisotopicMass, formula.MonoisotopicMass);
         }
 
         private static void WritePeptideToConsole(Peptide peptide)
         {
             ChemicalFormula formula;
             peptide.TryGetChemicalFormula(out formula);
-            Console.WriteLine("{0,-5} {1,-5} {2,-5}", peptide, formula, peptide.Mass.Monoisotopic);
+            Console.WriteLine("{0,-5} {1,-5} {2,-5}", peptide, formula, peptide.Mass.MonoisotopicMass);
         }
 
         private static void WriteFragmentToConsole(Fragment frag)
         {
-            Console.WriteLine("{0,-4} {1,-20}", frag, frag.Mass.Monoisotopic);
+            Console.WriteLine("{0,-4} {1,-20}", frag, frag.Mass.MonoisotopicMass);
         }
     }
 }

CSMSL.Examples/TrypticDigestion.cs

@@ -43,7 +43,7 @@ public static void Start(IProtease protease, int maxMissed = 3, int minLength =
                     foreach (Peptide peptide in protein.Digest(protease, maxMissed, minLength, maxLength))
                     {
                         peps.Add(peptide);
-                        allMzs.Add(peptide.Mass.ToMz(1)); // forces the calculation of the mass and thus chemical formula
+                        allMzs.Add(peptide.ToMz(2)); // forces the calculation of the mass and thus chemical formula
                     }
                     prots.Add(protein);
                 }

CSMSL.Tests/Chemistry/ChemicalFormulaTestFixture.cs

@@ -215,7 +215,7 @@ public void BasicChemicalFormulaMassMonoisotopic()
         {
             ChemicalFormula water = new ChemicalFormula("H2O");
 
-            Assert.AreEqual(2 * Constants.Hydrogen + Constants.Oxygen, water.Mass.Monoisotopic);
+            Assert.AreEqual(2 * Constants.Hydrogen + Constants.Oxygen, water.Mass.MonoisotopicMass);
         }
 
         [Test]
@@ -296,7 +296,7 @@ public void EmptyFormulaMassIsNotNull()
         [Test]
         public void EmptyFormulaMonoisotopicMassIsZero()
         {           
-            Assert.AreEqual(0.0, EmptyFormula.Mass.Monoisotopic);
+            Assert.AreEqual(0.0, EmptyFormula.Mass.MonoisotopicMass);
         }
 
         [Test]

CSMSL.Tests/Chemistry/MassTestFixture.cs

@@ -12,7 +12,7 @@ public void DefaultMassMonoisotopic()
         {
             Mass m = new Mass();
 
-            Assert.AreEqual(0.0, m.Monoisotopic);
+            Assert.AreEqual(0.0, m.MonoisotopicMass);
         }
 
         [Test]
@@ -28,7 +28,7 @@ public void MonoisotopicOnlyMassInConstructor()
         {
             Mass m = new Mass(524.342);
 
-            Assert.AreEqual(524.342, m.Monoisotopic);
+            Assert.AreEqual(524.342, m.MonoisotopicMass);
         }
 
         [Test]
@@ -44,7 +44,7 @@ public void MonoisotopicMassInConstructor()
         {
             Mass m = new Mass(524.342, 524.500);
 
-            Assert.AreEqual(524.342, m.Monoisotopic);
+            Assert.AreEqual(524.342, m.MonoisotopicMass);
         }
 
         [Test]

CSMSL.Tests/Proteomics/FragmentTestFixture.cs

@@ -69,55 +69,55 @@ public void FragmentCTerminalMod()
             MockPeptideEveryAminoAcid.SetModification(NamedChemicalFormula.TMT6plex, Terminus.C);
             Fragment fragment = MockPeptideEveryAminoAcid.Fragment(FragmentTypes.x, 1);          
 
-            fragment.Mass.Monoisotopic.Should().Equal(436.21608990639004);
+            fragment.Mass.MonoisotopicMass.Should().Equal(436.21608990639004);
         }
 
         [Test]       
         public void FragmentChemicalFormulaAIon()
         {
             Fragment fragment = MockPeptideEveryAminoAcid.Fragment(FragmentTypes.a, 1);          
 
-            fragment.Mass.Monoisotopic.Should().Equal(43.042199165149988);
+            fragment.Mass.MonoisotopicMass.Should().Equal(43.042199165149988);
         }
 
         [Test]
         public void FragmentChemicalFormulaBIon()
         {
             Fragment fragment = MockPeptideEveryAminoAcid.Fragment(FragmentTypes.b, 1);            
 
-            fragment.Mass.Monoisotopic.Should().Equal(71.037113784709987);
+            fragment.Mass.MonoisotopicMass.Should().Equal(71.037113784709987);
         }
 
         [Test]
         public void FragmentChemicalFormulaCIon()
         {
             Fragment fragment = MockPeptideEveryAminoAcid.Fragment(FragmentTypes.c, 1);
 
-            fragment.Mass.Monoisotopic.Should().Equal(88.063662885719992);
+            fragment.Mass.MonoisotopicMass.Should().Equal(88.063662885719992);
         }
 
         [Test]
         public void FragmentChemicalFormulaXIon()
         {
             Fragment fragment = MockPeptideEveryAminoAcid.Fragment(FragmentTypes.x, 1);
 
-            fragment.Mass.Monoisotopic.Should().Equal(207.05315777167004);
+            fragment.Mass.MonoisotopicMass.Should().Equal(207.05315777167004);
         }
 
         [Test]
         public void FragmentChemicalFormulaYIon()
         {
             Fragment fragment = MockPeptideEveryAminoAcid.Fragment(FragmentTypes.y, 1);
 
-            fragment.Mass.Monoisotopic.Should().Equal(181.07389321625004);
+            fragment.Mass.MonoisotopicMass.Should().Equal(181.07389321625004);
         }
 
         [Test]
         public void FragmentChemicalFormulaZIon()
         {
             Fragment fragment = MockPeptideEveryAminoAcid.Fragment(FragmentTypes.z, 1);
 
-            fragment.Mass.Monoisotopic.Should().Equal(164.04734411524004);
+            fragment.Mass.MonoisotopicMass.Should().Equal(164.04734411524004);
         }
     }
 }

CSMSL.Tests/Proteomics/PeptideTestFixture.cs

@@ -23,7 +23,7 @@ public void SetUp()
         [Test]
         public void PeptideMass()
         {
-            Assert.AreEqual(MockPeptideEveryAminoAcid.Mass.Monoisotopic, 2394.12490682513);
+            Assert.AreEqual(MockPeptideEveryAminoAcid.Mass.MonoisotopicMass, 2394.12490682513);
         }
 
         [Test]
@@ -161,7 +161,7 @@ public void ParseNamedChemicalNamedChemicalModification()
         { 
             Peptide peptide = new Peptide("T[TMT 6-plex]HGEAK[Acetyl]K[TMT 6-plex]");
 
-            peptide.Mass.Monoisotopic.Should().Equal(1269.74468058495);
+            Assert.AreEqual(1269.74468058495, peptide.MonoisotopicMass);
         }
 
         [Test]
@@ -186,7 +186,7 @@ public void ParseNamedChemicalModificationRegisterNew()
             NamedChemicalFormula.AddModification("C2H3NO", "Test");
             Peptide peptide = new Peptide("T[TMT 6-plex]HGEAK[Test]K[TMT 6-plex]");
 
-            peptide.Mass.Monoisotopic.Should().Equal(1284.7555796218198);
+            peptide.Mass.MonoisotopicMass.Should().Equal(1284.7555796218198);
         }
 
         [Test]

CSMSL.sln

@@ -20,6 +20,11 @@ Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "CSMSL.Tests", "CSMSL.Tests\
 EndProject
 Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "MzML", "CSMSL\IO\MzML\MzML.csproj", "{012434FB-88A9-4DEC-B887-5F64C0B481D4}"
 EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{59DB6973-98AE-4FAC-9D7D-DADEC35C9BA1}"
+	ProjectSection(SolutionItems) = preProject
+		Performance1.psess = Performance1.psess
+	EndProjectSection
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -122,4 +127,7 @@ Global
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
+	GlobalSection(Performance) = preSolution
+		HasPerformanceSessions = true
+	EndGlobalSection
 EndGlobal

CSMSL/Analysis/Identification/MSSearchEngine.cs

@@ -36,7 +36,7 @@ public abstract class MSSearchEngine
 
         public void LoadPeptides(IEnumerable<AminoAcidPolymer> peptides)
         {
-            _peptides = peptides.OrderBy(pep => pep.Mass.Monoisotopic).ToList();     
+            _peptides = peptides.OrderBy(pep => pep.Mass.MonoisotopicMass).ToList();     
         }
 
         public void AddVariableModification(IChemicalFormula modification, char residue)

CSMSL/Analysis/Quantitation/IsobaricTag.cs

@@ -24,7 +24,7 @@ public double reporterMass
         {
             get
             {
-                return _reporterFormula.Mass.Monoisotopic;
+                return _reporterFormula.Mass.MonoisotopicMass;
             }
         }
 

CSMSL/Analysis/Quantitation/QuantitationChannelSet.cs

@@ -109,8 +109,9 @@ public QuantitationChannelSet(string name, QuantitationChannelSetMassType massTy
 
         public IQuantitationChannel Add(IQuantitationChannel channel)
         {
-            _channels.Add(channel.ReporterMass.Monoisotopic, channel);
+            _channels.Add(channel.ReporterMass.MonoisotopicMass, channel);
             _totalMass.Add(channel.Mass);        
+
             return channel;
         }
 
@@ -122,7 +123,7 @@ public void Clear()
 
         public bool Remove(IQuantitationChannel channel)
         {
-            if (_channels.Remove(channel.Mass.Monoisotopic))
+            if (_channels.Remove(channel.Mass.MonoisotopicMass))
             {
                 _totalMass.Remove(channel.Mass);
                 return true;
@@ -159,7 +160,7 @@ public MassRange MassRange
         {
             get
             {
-                return new MassRange(LightestChannel.ReporterMass.Monoisotopic, HeaviestChannel.ReporterMass.Monoisotopic);
+                return new MassRange(LightestChannel.ReporterMass.MonoisotopicMass, HeaviestChannel.ReporterMass.MonoisotopicMass);
             }
         }
 
@@ -171,6 +172,11 @@ public int Count
             }
         }
 
+        public double MonoisotopicMass
+        {
+            get { throw new NotImplementedException(); }
+        }
+
         public override string ToString()
         {
             return Name;
@@ -384,5 +390,8 @@ private static void GetUniquePeptides_helper(IList<QuantitationChannelSet> sets,
         #endregion
 
 
+
+
+
     }
 }

CSMSL/CSMSL.csproj

@@ -97,6 +97,7 @@
     <Compile Include="Chemistry\IChemicalFormula.cs" />
     <Compile Include="Chemistry\Isotope.cs" />
     <Compile Include="Chemistry\PeriodicTable.cs" />
+    <Compile Include="ClassExtensions.cs" />
     <Compile Include="Constants.cs" />
     <Compile Include="Chemistry\IMass.cs" />
     <Compile Include="IO\Fasta.cs" />