Changeset 4639 for trunk/sources/HeuristicLab.Analysis

Timestamp:

10/22/10 03:17:02 (14 years ago)

Author:

swagner

Message:

Worked on allele frequency analysis (#1234)

Location:

trunk/sources/HeuristicLab.Analysis/3.3

Files:

• AlleleFrequencyAnalyzer.cs (modified) (5 diffs)
• AlleleFrequencyCollection.cs (moved) (moved from trunk/sources/HeuristicLab.Analysis/3.3/AlleleFrequencyArray.cs) (1 diff)
• AlleleFrequencyCollectionCollection.cs (added)
• HeuristicLab.Analysis-3.3.csproj (modified) (2 diffs)

trunk/sources/HeuristicLab.Analysis/3.3/AlleleFrequencyAnalyzer.cs

@@ -20 +20 @@
 #endregion
 
+using System.Collections.Generic;
 using System.Linq;
 using HeuristicLab.Core;
@@ -72 +73 @@
     }
 
+    private class AlleleFrequencyEqualityComparer : IEqualityComparer<AlleleFrequency> {
+      public bool Equals(AlleleFrequency x, AlleleFrequency y) {
+        return x.Id == y.Id;
+      }
+      public int GetHashCode(AlleleFrequency obj) {
+        return obj.GetHashCode();
+      }
+    }
+
     public override IOperation Apply() {
       int updateInterval = UpdateIntervalParameter.Value.Value;
@@ -110 +120 @@
                                                           bestAlleles.Any(a => a.Id == x.Key)));
 
+        // calculate dummy allele frequencies of alleles of best known solution which did not occur
+        var bestKnownFrequencies = bestKnownAlleles.Select(x => new AlleleFrequency(x.Id, 0, x.Impact, 0, true, false)).Except(frequencies, new AlleleFrequencyEqualityComparer());
+
         // fetch results collection
         ResultCollection results;
@@ -120 +133 @@
 
         // store allele frequencies
-        AlleleFrequencyArray frequenciesArray = new AlleleFrequencyArray(frequencies);
+        AlleleFrequencyCollection frequenciesCollection = new AlleleFrequencyCollection(bestKnownFrequencies.Concat(frequencies));
         if (!results.ContainsKey("Allele Frequencies"))
-          results.Add(new Result("Allele Frequencies", frequenciesArray));
+          results.Add(new Result("Allele Frequencies", frequenciesCollection));
         else
-          results["Allele Frequencies"].Value = frequenciesArray;
+          results["Allele Frequencies"].Value = frequenciesCollection;
 
         // store allele frequencies history
         if (storeHistory) {
           if (!results.ContainsKey("Allele Frequencies History")) {
-            ItemCollection<AlleleFrequencyArray> history = new ItemCollection<AlleleFrequencyArray>();
-            history.Add(frequenciesArray);
+            AlleleFrequencyCollectionCollection history = new AlleleFrequencyCollectionCollection();
+            history.Add(frequenciesCollection);
             results.Add(new Result("Allele Frequencies History", history));
           } else {
-            ((ItemCollection<AlleleFrequencyArray>)results["Allele Frequencies History"].Value).Add(frequenciesArray);
+            ((AlleleFrequencyCollectionCollection)results["Allele Frequencies History"].Value).Add(frequenciesCollection);
           }
         }
@@ -146 +159 @@
           allelesTable = (DataTable)results["Alleles"].Value;
         }
-        allelesTable.Rows["Unique Alleles"].Values.Add(frequenciesArray.Length);
+        allelesTable.Rows["Unique Alleles"].Values.Add(frequenciesCollection.Count);
       }
       return base.Apply();

trunk/sources/HeuristicLab.Analysis/3.3/AlleleFrequencyCollection.cs

@@ -26 +26 @@
 namespace HeuristicLab.Analysis {
   /// <summary>
-  /// Represents an array of allele frequencies.
+  /// Represents a collection of allele frequencies.
   /// </summary>
-  [Item("AlleleFrequencyArray", "Represents an array of allele frequencies.")]
+  [Item("AlleleFrequencyCollection", "Represents a collection of allele frequencies.")]
   [StorableClass]
-  public class AlleleFrequencyArray : ReadOnlyItemArray<AlleleFrequency> {
-    public AlleleFrequencyArray() : base() { }
-    public AlleleFrequencyArray(IEnumerable<AlleleFrequency> frequencies) : base(new ItemArray<AlleleFrequency>(frequencies)) { }
+  public class AlleleFrequencyCollection : ReadOnlyItemCollection<AlleleFrequency> {
+    public AlleleFrequencyCollection() : base() { }
+    public AlleleFrequencyCollection(IEnumerable<AlleleFrequency> frequencies) : base(new ItemCollection<AlleleFrequency>(frequencies)) { }
     [StorableConstructor]
-    protected AlleleFrequencyArray(bool deserializing) : base(deserializing) { }
+    protected AlleleFrequencyCollection(bool deserializing) : base(deserializing) { }
   }
 }

trunk/sources/HeuristicLab.Analysis/3.3/HeuristicLab.Analysis-3.3.csproj

@@ -110 +110 @@
   <ItemGroup>
     <None Include="HeuristicLabAnalysisPlugin.cs.frame" />
+    <Compile Include="AlleleFrequencyCollection.cs" />
     <Compile Include="BestAverageWorstQualityAnalyzer.cs" />
     <Compile Include="BestAverageWorstQualityCalculator.cs" />
@@ -116 +117 @@
     <Compile Include="Allele.cs" />
     <Compile Include="AlleleFrequency.cs" />
-    <Compile Include="AlleleFrequencyArray.cs" />
+    <Compile Include="AlleleFrequencyCollectionCollection.cs" />
     <Compile Include="QualityAnalyzer.cs" />
     <Compile Include="MinAverageMaxValueAnalyzer.cs" />