source: branches/histogram/HeuristicLab.Analysis/3.3/AlleleFrequencyAnalysis/AlleleFrequencyAnalyzer.cs @ 6055

Last change on this file since 6055 was 6055, checked in by abeham, 9 years ago

#1465

  • updated branch from trunk
File size: 13.1 KB
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1#region License Information
2/* HeuristicLab
3 * Copyright (C) 2002-2011 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
4 *
5 * This file is part of HeuristicLab.
6 *
7 * HeuristicLab is free software: you can redistribute it and/or modify
8 * it under the terms of the GNU General Public License as published by
9 * the Free Software Foundation, either version 3 of the License, or
10 * (at your option) any later version.
11 *
12 * HeuristicLab is distributed in the hope that it will be useful,
13 * but WITHOUT ANY WARRANTY; without even the implied warranty of
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
15 * GNU General Public License for more details.
16 *
17 * You should have received a copy of the GNU General Public License
18 * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
19 */
20#endregion
21
22using System.Collections.Generic;
23using System.Linq;
24using HeuristicLab.Common;
25using HeuristicLab.Core;
26using HeuristicLab.Data;
27using HeuristicLab.Operators;
28using HeuristicLab.Optimization;
29using HeuristicLab.Parameters;
30using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
31
32namespace HeuristicLab.Analysis {
33  /// <summary>
34  /// An operator for analyzing the frequency of alleles.
35  /// </summary>
36  [Item("AlleleFrequencyAnalyzer", "An operator for analyzing the frequency of alleles.")]
37  [StorableClass]
38  public abstract class AlleleFrequencyAnalyzer<T> : SingleSuccessorOperator, IAnalyzer where T : class, IItem {
39    public LookupParameter<BoolValue> MaximizationParameter {
40      get { return (LookupParameter<BoolValue>)Parameters["Maximization"]; }
41    }
42    public ScopeTreeLookupParameter<T> SolutionParameter {
43      get { return (ScopeTreeLookupParameter<T>)Parameters["Solution"]; }
44    }
45    public ScopeTreeLookupParameter<DoubleValue> QualityParameter {
46      get { return (ScopeTreeLookupParameter<DoubleValue>)Parameters["Quality"]; }
47    }
48    public LookupParameter<T> BestKnownSolutionParameter {
49      get { return (LookupParameter<T>)Parameters["BestKnownSolution"]; }
50    }
51    public ValueLookupParameter<ResultCollection> ResultsParameter {
52      get { return (ValueLookupParameter<ResultCollection>)Parameters["Results"]; }
53    }
54    public ValueParameter<BoolValue> StoreHistoryParameter {
55      get { return (ValueParameter<BoolValue>)Parameters["StoreHistory"]; }
56    }
57    public ValueParameter<IntValue> UpdateIntervalParameter {
58      get { return (ValueParameter<IntValue>)Parameters["UpdateInterval"]; }
59    }
60    public LookupParameter<IntValue> UpdateCounterParameter {
61      get { return (LookupParameter<IntValue>)Parameters["UpdateCounter"]; }
62    }
63
64    [StorableConstructor]
65    protected AlleleFrequencyAnalyzer(bool deserializing) : base(deserializing) { }
66    protected AlleleFrequencyAnalyzer(AlleleFrequencyAnalyzer<T> original, Cloner cloner) : base(original, cloner) { }
67    public AlleleFrequencyAnalyzer()
68      : base() {
69      Parameters.Add(new LookupParameter<BoolValue>("Maximization", "True if the problem is a maximization problem."));
70      Parameters.Add(new ScopeTreeLookupParameter<T>("Solution", "The solutions whose alleles should be analyzed."));
71      Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>("Quality", "The qualities of the solutions which should be analyzed."));
72      Parameters.Add(new LookupParameter<T>("BestKnownSolution", "The best known solution."));
73      Parameters.Add(new ValueLookupParameter<ResultCollection>("Results", "The result collection where the allele frequency analysis results should be stored."));
74      Parameters.Add(new ValueParameter<BoolValue>("StoreHistory", "True if the history of the allele frequency analysis should be stored.", new BoolValue(false)));
75      Parameters.Add(new ValueParameter<IntValue>("UpdateInterval", "The interval in which the allele frequency analysis should be applied.", new IntValue(1)));
76      Parameters.Add(new LookupParameter<IntValue>("UpdateCounter", "The value which counts how many times the operator was called since the last update.", "AlleleFrequencyAnalyzerUpdateCounter"));
77
78      MaximizationParameter.Hidden = true;
79      SolutionParameter.Hidden = true;
80      QualityParameter.Hidden = true;
81      BestKnownSolutionParameter.Hidden = true;
82      ResultsParameter.Hidden = true;
83      UpdateCounterParameter.Hidden = true;
84    }
85
86    #region AlleleFrequencyIdEqualityComparer
87    private class AlleleFrequencyIdEqualityComparer : IEqualityComparer<AlleleFrequency> {
88      public bool Equals(AlleleFrequency x, AlleleFrequency y) {
89        return x.Id == y.Id;
90      }
91      public int GetHashCode(AlleleFrequency obj) {
92        return obj.Id.GetHashCode();
93      }
94    }
95    #endregion
96
97    public override IOperation Apply() {
98      int updateInterval = UpdateIntervalParameter.Value.Value;
99      IntValue updateCounter = UpdateCounterParameter.ActualValue;
100      if (updateCounter == null) {
101        updateCounter = new IntValue(updateInterval);
102        UpdateCounterParameter.ActualValue = updateCounter;
103      } else updateCounter.Value++;
104
105      if (updateCounter.Value == updateInterval) {
106        updateCounter.Value = 0;
107
108        bool max = MaximizationParameter.ActualValue.Value;
109        ItemArray<T> solutions = SolutionParameter.ActualValue;
110        ItemArray<DoubleValue> qualities = QualityParameter.ActualValue;
111        T bestKnownSolution = BestKnownSolutionParameter.ActualValue;
112        bool storeHistory = StoreHistoryParameter.Value.Value;
113
114        // calculate index of current best solution
115        int bestIndex = -1;
116        if (!max) {
117          bestIndex = qualities
118            .Select((x, index) => new { index, x.Value })
119            .OrderBy(x => x.Value)
120            .First().index;
121        } else {
122          bestIndex = qualities
123            .Select((x, index) => new { index, x.Value })
124            .OrderByDescending(x => x.Value)
125            .First().index;
126        }
127
128        // calculate allels of current best and (if available) best known solution
129        Allele[] bestAlleles = CalculateAlleles(solutions[bestIndex]);
130        Allele[] bestKnownAlleles = null;
131        if (bestKnownSolution != null)
132          bestKnownAlleles = CalculateAlleles(bestKnownSolution);
133
134        // calculate allele frequencies
135        var frequencies = solutions.SelectMany((s, index) => CalculateAlleles(s).Select(a => new { Allele = a, Quality = qualities[index] })).
136                          GroupBy(x => x.Allele.Id).
137                          Select(x => new AlleleFrequency(x.Key,
138                                                          x.Count() / ((double)solutions.Length),
139                                                          x.Average(a => a.Allele.Impact),
140                                                          x.Average(a => a.Quality.Value),
141                                                          bestKnownAlleles == null ? false : bestKnownAlleles.Any(a => a.Id == x.Key),
142                                                          bestAlleles.Any(a => a.Id == x.Key)));
143
144        // calculate dummy allele frequencies of alleles of best known solution which did not occur
145        if (bestKnownAlleles != null) {
146          var bestKnownFrequencies = bestKnownAlleles.Select(x => new AlleleFrequency(x.Id, 0, x.Impact, 0, true, false)).Except(frequencies, new AlleleFrequencyIdEqualityComparer());
147          frequencies = frequencies.Concat(bestKnownFrequencies);
148        }
149
150        // fetch results collection
151        ResultCollection results;
152        if (!ResultsParameter.ActualValue.ContainsKey(Name + " Results")) {
153          results = new ResultCollection();
154          ResultsParameter.ActualValue.Add(new Result(Name + " Results", results));
155        } else {
156          results = (ResultCollection)ResultsParameter.ActualValue[Name + " Results"].Value;
157        }
158
159        // store allele frequencies
160        AlleleFrequencyCollection frequenciesCollection = new AlleleFrequencyCollection(frequencies);
161        if (!results.ContainsKey("Allele Frequencies"))
162          results.Add(new Result("Allele Frequencies", frequenciesCollection));
163        else
164          results["Allele Frequencies"].Value = frequenciesCollection;
165
166        // store allele frequencies history
167        if (storeHistory) {
168          if (!results.ContainsKey("Allele Frequencies History")) {
169            AlleleFrequencyCollectionHistory history = new AlleleFrequencyCollectionHistory();
170            history.Add(frequenciesCollection);
171            results.Add(new Result("Allele Frequencies History", history));
172          } else {
173            ((AlleleFrequencyCollectionHistory)results["Allele Frequencies History"].Value).Add(frequenciesCollection);
174          }
175        }
176
177        // store alleles data table
178        DataTable allelesTable;
179        if (!results.ContainsKey("Alleles")) {
180          allelesTable = new DataTable("Alleles");
181          allelesTable.VisualProperties.XAxisTitle = "Iteration";
182          allelesTable.VisualProperties.YAxisTitle = "Number of Alleles";
183          allelesTable.VisualProperties.SecondYAxisTitle = "Number of Alleles";
184
185          allelesTable.Rows.Add(new DataRow("Unique Alleles"));
186          allelesTable.Rows["Unique Alleles"].VisualProperties.StartIndexZero = true;
187
188          allelesTable.Rows.Add(new DataRow("Unique Alleles of Best Known Solution", null));
189          allelesTable.Rows["Unique Alleles of Best Known Solution"].VisualProperties.SecondYAxis = true;
190          allelesTable.Rows["Unique Alleles of Best Known Solution"].VisualProperties.StartIndexZero = true;
191
192          allelesTable.Rows.Add(new DataRow("Fixed Alleles", null));
193          allelesTable.Rows["Fixed Alleles"].VisualProperties.SecondYAxis = true;
194          allelesTable.Rows["Fixed Alleles"].VisualProperties.StartIndexZero = true;
195
196          allelesTable.Rows.Add(new DataRow("Fixed Alleles of Best Known Solution", null));
197          allelesTable.Rows["Fixed Alleles of Best Known Solution"].VisualProperties.SecondYAxis = true;
198          allelesTable.Rows["Fixed Alleles of Best Known Solution"].VisualProperties.StartIndexZero = true;
199
200          allelesTable.Rows.Add(new DataRow("Lost Alleles of Best Known Solution", null));
201          allelesTable.Rows["Lost Alleles of Best Known Solution"].VisualProperties.SecondYAxis = true;
202          allelesTable.Rows["Lost Alleles of Best Known Solution"].VisualProperties.StartIndexZero = true;
203
204          results.Add(new Result("Alleles", allelesTable));
205        } else {
206          allelesTable = (DataTable)results["Alleles"].Value;
207        }
208
209        int fixedAllelesCount = frequenciesCollection.Where(x => x.Frequency == 1).Count();
210        var relevantAlleles = frequenciesCollection.Where(x => x.ContainedInBestKnownSolution);
211        int relevantAllelesCount = relevantAlleles.Count();
212        int fixedRelevantAllelesCount = relevantAlleles.Where(x => x.Frequency == 1).Count();
213        int lostRelevantAllelesCount = relevantAlleles.Where(x => x.Frequency == 0).Count();
214        int uniqueRelevantAllelesCount = relevantAllelesCount - lostRelevantAllelesCount;
215        allelesTable.Rows["Unique Alleles"].Values.Add(frequenciesCollection.Count);
216        allelesTable.Rows["Unique Alleles of Best Known Solution"].Values.Add(uniqueRelevantAllelesCount);
217        allelesTable.Rows["Fixed Alleles"].Values.Add(fixedAllelesCount);
218        allelesTable.Rows["Fixed Alleles of Best Known Solution"].Values.Add(fixedRelevantAllelesCount);
219        allelesTable.Rows["Lost Alleles of Best Known Solution"].Values.Add(lostRelevantAllelesCount);
220
221        // store alleles values
222        if (!results.ContainsKey("Unique Alleles"))
223          results.Add(new Result("Unique Alleles", new DoubleValue(frequenciesCollection.Count)));
224        else
225          ((DoubleValue)results["Unique Alleles"].Value).Value = frequenciesCollection.Count;
226
227        if (!results.ContainsKey("Unique Alleles of Best Known Solution"))
228          results.Add(new Result("Unique Alleles of Best Known Solution", new DoubleValue(uniqueRelevantAllelesCount)));
229        else
230          ((DoubleValue)results["Unique Alleles of Best Known Solution"].Value).Value = uniqueRelevantAllelesCount;
231
232        if (!results.ContainsKey("Fixed Alleles"))
233          results.Add(new Result("Fixed Alleles", new DoubleValue(fixedAllelesCount)));
234        else
235          ((DoubleValue)results["Fixed Alleles"].Value).Value = fixedAllelesCount;
236
237        if (!results.ContainsKey("Fixed Alleles of Best Known Solution"))
238          results.Add(new Result("Fixed Alleles of Best Known Solution", new DoubleValue(fixedRelevantAllelesCount)));
239        else
240          ((DoubleValue)results["Fixed Alleles of Best Known Solution"].Value).Value = fixedRelevantAllelesCount;
241
242        if (!results.ContainsKey("Lost Alleles of Best Known Solution"))
243          results.Add(new Result("Lost Alleles of Best Known Solution", new DoubleValue(lostRelevantAllelesCount)));
244        else
245          ((DoubleValue)results["Lost Alleles of Best Known Solution"].Value).Value = lostRelevantAllelesCount;
246      }
247      return base.Apply();
248    }
249
250    protected abstract Allele[] CalculateAlleles(T solution);
251  }
252}
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