Class rename and diagram

smith-chem-wisc · Dec 11, 2023 · cda0872 · cda0872
1 parent 18aecce
commit cda0872
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Showing 4 changed files with 52 additions and 7 deletions.
diff --git a/.../MachineLearning/ChronologerDictionary.cs → mzLib/MachineLearning/DictionaryBuilder.cs b/.../MachineLearning/ChronologerDictionary.cs → mzLib/MachineLearning/DictionaryBuilder.cs
@@ -4,7 +4,10 @@
 
 namespace UsefulProteomicsDatabases
 {
-    public static class ChronologerDictionary
+    /// <summary>
+    /// This class provides static methods to build dictionaries for different models.
+    /// </summary>
+    public static class DictionaryBuilder
     {
         public static Dictionary<(char, string), int>
             GetChronologerDictionary(TypeOfDictionary dict)

diff --git a/mzLib/MachineLearning/MachineLearningDiagram.cd b/mzLib/MachineLearning/MachineLearningDiagram.cd
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="utf-8"?>
+<ClassDiagram MajorVersion="1" MinorVersion="1">
+  <Class Name="MachineLearning.DeepTorch">
+    <Position X="8" Y="2" Width="4.5" />
+    <TypeIdentifier>
+      <HashCode>AAAgAgAAAACAAgAAAAAxAAAIICgAIAQAAIAACABCAAg=</HashCode>
+      <FileName>DeepTorch.cs</FileName>
+    </TypeIdentifier>
+  </Class>
+  <Class Name="MachineLearning.TorchDataset">
+    <Position X="14.25" Y="2.5" Width="3" />
+    <TypeIdentifier>
+      <HashCode>AAAAAAACAAAAAAAAAAAAAAQAAAAAABAAAAAAQAAAAAA=</HashCode>
+      <FileName>TorchDataset.cs</FileName>
+    </TypeIdentifier>
+  </Class>
+  <Class Name="MachineLearning.RetentionTimePredictionModels.Chronologer">
+    <Position X="8.75" Y="8" Width="3.25" />
+    <TypeIdentifier>
+      <HashCode>ABIgAgAIAACAAAAAAAAwQAAIOCAAAEAAAIAACAACACg=</HashCode>
+      <FileName>RetentionTimePredictionModels\Chronologer.cs</FileName>
+    </TypeIdentifier>
+  </Class>
+  <Class Name="UsefulProteomicsDatabases.DictionaryBuilder">
+    <Position X="13.75" Y="8" Width="4.25" />
+    <Compartments>
+      <Compartment Name="Nested Types" Collapsed="false" />
+    </Compartments>
+    <NestedTypes>
+      <Enum Name="UsefulProteomicsDatabases.DictionaryBuilder.TypeOfDictionary" Collapsed="true">
+        <TypeIdentifier>
+          <NewMemberFileName>DictionaryBuilder.cs</NewMemberFileName>
+        </TypeIdentifier>
+      </Enum>
+    </NestedTypes>
+    <TypeIdentifier>
+      <HashCode>AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=</HashCode>
+      <FileName>DictionaryBuilder.cs</FileName>
+    </TypeIdentifier>
+  </Class>
+  <Font Name="Segoe UI" Size="9" />
+</ClassDiagram>
diff --git a/mzLib/MachineLearning/RetentionTimePredictionModels/Chronologer.cs b/mzLib/MachineLearning/RetentionTimePredictionModels/Chronologer.cs
@@ -7,7 +7,7 @@
 using TorchSharp;
 using TorchSharp.Modules;
 using TorchSharp.Utils;
-using static UsefulProteomicsDatabases.ChronologerDictionary;
+using static UsefulProteomicsDatabases.DictionaryBuilder;
 
 namespace MachineLearning.RetentionTimePredictionModels
 {

diff --git a/mzLib/Test/TestChronologer.cs b/mzLib/Test/TestChronologer.cs
@@ -16,7 +16,7 @@ public class TestChronologer
         public void TestChronologerMethods()
         {
             var dictionary =
-                ChronologerDictionary.GetChronologerDictionary(ChronologerDictionary.TypeOfDictionary.Chronologer);
+                DictionaryBuilder.GetChronologerDictionary(DictionaryBuilder.TypeOfDictionary.Chronologer);
             var chronologer = new Chronologer(dictionary, Path.Combine(AppDomain.CurrentDomain.BaseDirectory,
                 "RetentionTimePredictionModels",
                 "Chronologer_20220601193755_TorchSharp.dat"));
@@ -47,7 +47,7 @@ public void TestChronologerMethods()
         public void TestDatasets()
         {
             var dictionary =
-                ChronologerDictionary.GetChronologerDictionary(ChronologerDictionary.TypeOfDictionary.Chronologer);
+                DictionaryBuilder.GetChronologerDictionary(DictionaryBuilder.TypeOfDictionary.Chronologer);
 
             var chronologer = new Chronologer(dictionary, Path.Combine(AppDomain.CurrentDomain.BaseDirectory,
                 "RetentionTimePredictionModels",
@@ -115,7 +115,7 @@ public void TestDatasets()
         public void TestTensorize()
         {
             var dictionary =
-                ChronologerDictionary.GetChronologerDictionary(ChronologerDictionary.TypeOfDictionary.Chronologer);
+                DictionaryBuilder.GetChronologerDictionary(DictionaryBuilder.TypeOfDictionary.Chronologer);
 
             var chronologer = new Chronologer(dictionary, Path.Combine(AppDomain.CurrentDomain.BaseDirectory,
                                "RetentionTimePredictionModels",
@@ -136,7 +136,7 @@ public void TestTensorize()
         public void TestForwardPass()
         {
             var dictionary =
-                ChronologerDictionary.GetChronologerDictionary(ChronologerDictionary.TypeOfDictionary.Chronologer);
+                DictionaryBuilder.GetChronologerDictionary(DictionaryBuilder.TypeOfDictionary.Chronologer);
 
             var chronologer = new Chronologer(dictionary, Path.Combine(AppDomain.CurrentDomain.BaseDirectory,
                 "RetentionTimePredictionModels",
@@ -155,7 +155,7 @@ public void TestForwardPass()
         public void TestTrainMethod()
         {
             var dictionary =
-                ChronologerDictionary.GetChronologerDictionary(ChronologerDictionary.TypeOfDictionary.Chronologer);
+                DictionaryBuilder.GetChronologerDictionary(DictionaryBuilder.TypeOfDictionary.Chronologer);
 
             var chronologer = new Chronologer(dictionary, Path.Combine(AppDomain.CurrentDomain.BaseDirectory,
                                "RetentionTimePredictionModels",