Changeset 4631

Timestamp:

10/21/10 02:58:15 (14 years ago)

Author:

swagner

Message:

Worked on allele frequency analysis (#1234)

Location:

trunk/sources

Files:

• HeuristicLab.Analysis.Views/3.3/AlleleFrequencyArrayView.Designer.cs (modified) (3 diffs)
• HeuristicLab.Analysis.Views/3.3/AlleleFrequencyArrayView.cs (modified) (4 diffs)
• HeuristicLab.Analysis.Views/3.3/HeuristicLab.Analysis.Views-3.3.csproj (modified) (2 diffs)
• HeuristicLab.Analysis.Views/3.3/HeuristicLabAnalysisViewsPlugin.cs.frame (modified) (1 diff)
• HeuristicLab.Analysis/3.3/AlleleFrequencyAnalyzer.cs (modified) (2 diffs)

trunk/sources/HeuristicLab.Analysis.Views/3.3/AlleleFrequencyArrayView.Designer.cs

@@ -47 +47 @@
       System.Windows.Forms.DataVisualization.Charting.ChartArea chartArea1 = new System.Windows.Forms.DataVisualization.Charting.ChartArea();
       System.Windows.Forms.DataVisualization.Charting.Legend legend1 = new System.Windows.Forms.DataVisualization.Charting.Legend();
-      System.Windows.Forms.DataVisualization.Charting.Series series1 = new System.Windows.Forms.DataVisualization.Charting.Series();
-      this.chart = new System.Windows.Forms.DataVisualization.Charting.Chart();
+      System.Windows.Forms.DataVisualization.Charting.Title title1 = new System.Windows.Forms.DataVisualization.Charting.Title();
+      this.chart = new HeuristicLab.Visualization.ChartControlsExtensions.EnhancedChart();
       ((System.ComponentModel.ISupportInitialize)(this.chart)).BeginInit();
       this.SuspendLayout();
@@ -59 +59 @@
       this.chart.BorderlineColor = System.Drawing.Color.Black;
       this.chart.BorderlineDashStyle = System.Windows.Forms.DataVisualization.Charting.ChartDashStyle.Solid;
+      chartArea1.AxisX.IntervalAutoMode = System.Windows.Forms.DataVisualization.Charting.IntervalAutoMode.VariableCount;
+      chartArea1.AxisX.LabelAutoFitStyle = ((System.Windows.Forms.DataVisualization.Charting.LabelAutoFitStyles)((System.Windows.Forms.DataVisualization.Charting.LabelAutoFitStyles.IncreaseFont | System.Windows.Forms.DataVisualization.Charting.LabelAutoFitStyles.DecreaseFont)));
+      chartArea1.AxisX.LabelStyle.Angle = 90;
+      chartArea1.AxisX.Title = "Alleles";
+      chartArea1.AxisY.Maximum = 1D;
+      chartArea1.AxisY.Minimum = 0D;
+      chartArea1.AxisY.Title = "Relative Frequency";
+      chartArea1.AxisY2.Title = "Average Solution Quality";
       chartArea1.CursorX.IsUserEnabled = true;
       chartArea1.CursorX.IsUserSelectionEnabled = true;
       chartArea1.CursorY.IsUserEnabled = true;
       chartArea1.CursorY.IsUserSelectionEnabled = true;
-      chartArea1.Name = "ChartArea1";
+      chartArea1.Name = "Default";
       this.chart.ChartAreas.Add(chartArea1);
       legend1.Docking = System.Windows.Forms.DataVisualization.Charting.Docking.Top;
-      legend1.Name = "Legend1";
+      legend1.Name = "Default";
       this.chart.Legends.Add(legend1);
       this.chart.Location = new System.Drawing.Point(0, 0);
       this.chart.Name = "chart";
-      series1.ChartArea = "ChartArea1";
-      series1.Legend = "Legend1";
-      series1.Name = "Series1";
-      this.chart.Series.Add(series1);
       this.chart.Size = new System.Drawing.Size(498, 359);
-      this.chart.TabIndex = 4;
-      this.chart.Text = "chart1";
+      this.chart.TabIndex = 0;
+      this.chart.Text = "chart";
+      title1.Name = "Default";
+      title1.Text = "Allele Frequencies";
+      this.chart.Titles.Add(title1);
+      this.chart.CustomizeLegend += new System.EventHandler<System.Windows.Forms.DataVisualization.Charting.CustomizeLegendEventArgs>(this.chart_CustomizeLegend);
+      this.chart.MouseDown += new System.Windows.Forms.MouseEventHandler(this.chart_MouseDown);
+      this.chart.MouseMove += new System.Windows.Forms.MouseEventHandler(this.chart_MouseMove);
       // 
       // AlleleFrequencyArrayView
@@ -92 +102 @@
     #endregion
 
-    private System.Windows.Forms.DataVisualization.Charting.Chart chart;
+    protected HeuristicLab.Visualization.ChartControlsExtensions.EnhancedChart chart;
 
   }

trunk/sources/HeuristicLab.Analysis.Views/3.3/AlleleFrequencyArrayView.cs

@@ -20 +20 @@
 #endregion
 
+using System.Collections.Generic;
+using System.Drawing;
+using System.Linq;
 using System.Windows.Forms;
 using System.Windows.Forms.DataVisualization.Charting;
@@ -29 +32 @@
   [Content(typeof(AlleleFrequencyArray), true)]
   public partial class AlleleFrequencyArrayView : ItemView {
+    private List<Series> invisibleSeries;
+
     public new AlleleFrequencyArray Content {
       get { return (AlleleFrequencyArray)base.Content; }
@@ -36 +41 @@
     public AlleleFrequencyArrayView() {
       InitializeComponent();
-    }
-
-    protected override void DeregisterContentEvents() {
-      // ...
-      base.DeregisterContentEvents();
-    }
-
-    protected override void RegisterContentEvents() {
-      base.RegisterContentEvents();
-      // ...
+      invisibleSeries = new List<Series>();
     }
 
     protected override void OnContentChanged() {
       base.OnContentChanged();
-      chart.Titles.Clear();
-      chart.Series.Clear();
-      chart.DataSource = null;
-      if (Content != null)
-        PopulateChart();
+      if (Content == null) {
+        chart.Series.Clear();
+        chart.DataSource = null;
+        invisibleSeries.Clear();
+      } else {
+        if (chart.Series.Count == 0) CreateSeries();
+        chart.DataSource = Content.Select(x => new {
+          Id = x.Id,
+          BestKnownFrequency = x.ContainedInBestKnownSolution ? x.Frequency : 0,
+          Frequency = !x.ContainedInBestKnownSolution ? x.Frequency : 0,
+          Quality = x.AverageSolutionQuality,
+          Impact = x.AverageImpact
+        }).OrderBy(x => x.Impact).ToArray();
+        UpdateSeries();
+      }
     }
 
@@ -62 +68 @@
     }
 
-    private void PopulateChart() {
-      chart.Titles.Add(new Title("Allele Frequencies", Docking.Top));
-      chart.DataSource = Content;
-      Series frequencies = new Series("Frequencies");
-      frequencies.ChartType = SeriesChartType.Column;
-      frequencies.XValueMember = "Id";
-      frequencies.XValueType = ChartValueType.String;
-      frequencies.YValueMembers = "Frequency";
-      frequencies.YValueType = ChartValueType.Double;
-      frequencies.YAxisType = AxisType.Primary;
-      frequencies.ToolTip = "X = #INDEX, Y = #VAL";
-      chart.Series.Add(frequencies);
+    protected virtual void CreateSeries() {
+      Series bestKnown = new Series("Alleles of Best Known Solution");
+      bestKnown.ChartType = SeriesChartType.StackedColumn;
+      bestKnown.XValueMember = "Id";
+      bestKnown.XValueType = ChartValueType.String;
+      bestKnown.YValueMembers = "BestKnownFrequency";
+      bestKnown.YValueType = ChartValueType.Double;
+      bestKnown.YAxisType = AxisType.Primary;
+      bestKnown.ToolTip = "X = #LABEL, Y = #VAL";
+      chart.Series.Add(bestKnown);
+
+      Series others = new Series("Other Alleles");
+      others.ChartType = SeriesChartType.StackedColumn;
+      others.XValueMember = "Id";
+      others.XValueType = ChartValueType.String;
+      others.YValueMembers = "Frequency";
+      others.YValueType = ChartValueType.Double;
+      others.YAxisType = AxisType.Primary;
+      others.ToolTip = "X = #LABEL, Y = #VAL";
+      chart.Series.Add(others);
+
       Series qualities = new Series("Average Solution Qualities");
       qualities.ChartType = SeriesChartType.FastLine;
       qualities.XValueMember = "Id";
       qualities.XValueType = ChartValueType.String;
-      qualities.YValueMembers = "AverageSolutionQuality";
+      qualities.YValueMembers = "Quality";
       qualities.YValueType = ChartValueType.Double;
       qualities.YAxisType = AxisType.Secondary;
-      qualities.ToolTip = "X = #INDEX, Y = #VAL";
+      qualities.ToolTip = "X = #LABEL, Y = #VAL";
       chart.Series.Add(qualities);
+
+      Series impacts = new Series("Average Impact");
+      impacts.ChartType = SeriesChartType.FastLine;
+      impacts.XValueMember = "Id";
+      impacts.XValueType = ChartValueType.String;
+      impacts.YValueMembers = "Impact";
+      impacts.YValueType = ChartValueType.Double;
+      impacts.YAxisType = AxisType.Secondary;
+      impacts.ToolTip = "X = #LABEL, Y = #VAL";
+      chart.Series.Add(impacts);
     }
+
+    protected virtual void UpdateSeries() {
+      chart.DataBind();
+
+      if (invisibleSeries.Contains(chart.Series["Alleles of Best Known Solution"]))
+        chart.Series["Alleles of Best Known Solution"].Points.Clear();
+      chart.DataManipulator.Filter(CompareMethod.EqualTo, 0, chart.Series["Alleles of Best Known Solution"]);
+
+      if (invisibleSeries.Contains(chart.Series["Other Alleles"]))
+        chart.Series["Other Alleles"].Points.Clear();
+      chart.DataManipulator.Filter(CompareMethod.EqualTo, 0, chart.Series["Other Alleles"]);
+
+      if (invisibleSeries.Contains(chart.Series["Average Solution Qualities"]))
+        chart.Series["Average Solution Qualities"].Points.Clear();
+      chart.DataManipulator.Filter(CompareMethod.EqualTo, 0, chart.Series["Average Solution Qualities"]);
+
+      if (invisibleSeries.Contains(chart.Series["Average Impact"]))
+        chart.Series["Average Impact"].Points.Clear();
+      chart.DataManipulator.Filter(CompareMethod.EqualTo, 0, chart.Series["Average Impact"]);
+    }
+
+    #region Chart Events
+    protected virtual void chart_MouseDown(object sender, MouseEventArgs e) {
+      HitTestResult result = chart.HitTest(e.X, e.Y);
+      if (result.ChartElementType == ChartElementType.LegendItem) {
+        ToggleSeriesVisible(result.Series);
+      }
+    }
+
+    protected virtual void ToggleSeriesVisible(Series series) {
+      if (!invisibleSeries.Contains(series))
+        invisibleSeries.Add(series);
+      else
+        invisibleSeries.Remove(series);
+      UpdateSeries();
+    }
+
+    protected virtual void chart_MouseMove(object sender, MouseEventArgs e) {
+      HitTestResult result = chart.HitTest(e.X, e.Y);
+      if (result.ChartElementType == ChartElementType.LegendItem)
+        this.Cursor = Cursors.Hand;
+      else
+        this.Cursor = Cursors.Default;
+    }
+
+    protected virtual void chart_CustomizeLegend(object sender, CustomizeLegendEventArgs e) {
+      foreach (LegendItem legendItem in e.LegendItems) {
+        var series = chart.Series[legendItem.SeriesName];
+        if (series != null) {
+          bool seriesIsInvisible = invisibleSeries.Contains(series);
+          foreach (LegendCell cell in legendItem.Cells) {
+            cell.ForeColor = seriesIsInvisible ? Color.Gray : Color.Black;
+          }
+        }
+      }
+    }
+    #endregion
   }
 }

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

@@ -94 +94 @@
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="HeuristicLab.Common.Resources-3.3, Version=3.2.0.0, Culture=neutral, PublicKeyToken=ba48961d6f65dcec, processorArchitecture=MSIL" />
+    <Reference Include="HeuristicLab.Data.Views-3.3">
+      <HintPath>..\..\HeuristicLab.Data.Views\3.3\bin\Debug\HeuristicLab.Data.Views-3.3.dll</HintPath>
+    </Reference>
+    <Reference Include="HeuristicLab.Optimization-3.3, Version=3.3.0.0, Culture=neutral, PublicKeyToken=ba48961d6f65dcec, processorArchitecture=MSIL" />
     <Reference Include="System" />
     <Reference Include="System.Core">
@@ -170 +175 @@
       <Name>HeuristicLab.MainForm-3.3</Name>
     </ProjectReference>
+    <ProjectReference Include="..\..\HeuristicLab.Optimization.Views\3.3\HeuristicLab.Optimization.Views-3.3.csproj">
+      <Project>{662B4B15-8F4D-4AE5-B3EB-D91C215F5AF2}</Project>
+      <Name>HeuristicLab.Optimization.Views-3.3</Name>
+    </ProjectReference>
     <ProjectReference Include="..\..\HeuristicLab.PluginInfrastructure\3.3\HeuristicLab.PluginInfrastructure-3.3.csproj">
       <Project>{94186A6A-5176-4402-AE83-886557B53CCA}</Project>
       <Name>HeuristicLab.PluginInfrastructure-3.3</Name>
+    </ProjectReference>
+    <ProjectReference Include="..\..\HeuristicLab.Visualization.ChartControlsExtensions\3.3\HeuristicLab.Visualization.ChartControlsExtensions-3.3.csproj">
+      <Project>{315BDA09-3F4F-49B3-9790-B37CFC1C5750}</Project>
+      <Name>HeuristicLab.Visualization.ChartControlsExtensions-3.3</Name>
     </ProjectReference>
   </ItemGroup>

trunk/sources/HeuristicLab.Analysis.Views/3.3/HeuristicLabAnalysisViewsPlugin.cs.frame

@@ -36 +36 @@
   [PluginDependency("HeuristicLab.MainForm", "3.3")]
   [PluginDependency("HeuristicLab.MainForm.WindowsForms", "3.3")]
+  [PluginDependency("HeuristicLab.Visualization.ChartControlsExtensions", "3.3")]
   public class HeuristicLabAnalysisViewsPlugin : PluginBase {
   }

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

@@ -44 +44 @@
       get { return (ScopeTreeLookupParameter<DoubleValue>)Parameters["Quality"]; }
     }
+    public LookupParameter<T> BestKnownSolutionParameter {
+      get { return (LookupParameter<T>)Parameters["BestKnownSolution"]; }
+    }
     public ValueLookupParameter<ResultCollection> ResultsParameter {
       get { return (ValueLookupParameter<ResultCollection>)Parameters["Results"]; }
     }
-    public LookupParameter<T> BestKnownSolutionParameter {
-      get { return (LookupParameter<T>)Parameters["BestKnownSolution"]; }
+    public ValueParameter<BoolValue> StoreAlleleFrequenciesHistoryParameter {
+      get { return (ValueParameter<BoolValue>)Parameters["StoreAlleleFrequenciesHistory"]; }
     }
-    public LookupParameter<AlleleFrequencyArray> AlleleFrequenciesParameter {
-      get { return (LookupParameter<AlleleFrequencyArray>)Parameters["AlleleFrequencies"]; }
+    public ValueParameter<IntValue> UpdateIntervalParameter {
+      get { return (ValueParameter<IntValue>)Parameters["UpdateInterval"]; }
+    }
+    public LookupParameter<IntValue> UpdateCounterParameter {
+      get { return (LookupParameter<IntValue>)Parameters["UpdateCounter"]; }
     }
 
@@ -59 +65 @@
       Parameters.Add(new ScopeTreeLookupParameter<T>("Solution", "The solutions whose alleles should be analyzed."));
       Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>("Quality", "The qualities of the solutions which should be analyzed."));
+      Parameters.Add(new LookupParameter<T>("BestKnownSolution", "The best known solution."));
       Parameters.Add(new ValueLookupParameter<ResultCollection>("Results", "The result collection where the allele frequency analysis results should be stored."));
-      Parameters.Add(new LookupParameter<T>("BestKnownSolution", "The best known solution."));
-      Parameters.Add(new LookupParameter<AlleleFrequencyArray>("AlleleFrequencies", "The frequencies of the alleles in the current iteration."));
+      Parameters.Add(new ValueParameter<BoolValue>("StoreAlleleFrequenciesHistory", "True if the history of all allele frequencies should be stored.", new BoolValue(false)));
+      Parameters.Add(new ValueParameter<IntValue>("UpdateInterval", "The interval in which the allele frequency analysis should be applied.", new IntValue(1)));
+      Parameters.Add(new LookupParameter<IntValue>("UpdateCounter", "The value which counts how many times the operator was called since the last update."));
     }
 
     public override IOperation Apply() {
-      bool max = MaximizationParameter.ActualValue.Value;
-      ItemArray<T> solutions = SolutionParameter.ActualValue;
-      ItemArray<DoubleValue> qualities = QualityParameter.ActualValue;
-      ResultCollection results = ResultsParameter.ActualValue;
-      T bestKnownSolution = BestKnownSolutionParameter.ActualValue;
+      int updateInterval = UpdateIntervalParameter.Value.Value;
+      IntValue updateCounter = UpdateCounterParameter.ActualValue;
+      if (updateCounter == null) {
+        updateCounter = new IntValue(updateInterval);
+        UpdateCounterParameter.ActualValue = updateCounter;
+      } else updateCounter.Value++;
 
-      int bestIndex = -1;
-      if (!max) bestIndex = qualities.Select((x, index) => new { index, x.Value }).OrderBy(x => x.Value).First().index;
-      else bestIndex = qualities.Select((x, index) => new { index, x.Value }).OrderByDescending(x => x.Value).First().index;
+      if (updateCounter.Value == updateInterval) {
+        updateCounter.Value = 0;
 
-      Allele[] bestAlleles = CalculateAlleles(solutions[bestIndex]);
-      Allele[] bestKnownAlleles = null;
-      if (bestKnownSolution != null) {
-        bestKnownAlleles = CalculateAlleles(bestKnownSolution);
+        bool max = MaximizationParameter.ActualValue.Value;
+        ItemArray<T> solutions = SolutionParameter.ActualValue;
+        ItemArray<DoubleValue> qualities = QualityParameter.ActualValue;
+        T bestKnownSolution = BestKnownSolutionParameter.ActualValue;
+        bool storeHistory = StoreAlleleFrequenciesHistoryParameter.Value.Value;
+
+        // calculate index of current best solution
+        int bestIndex = -1;
+        if (!max) bestIndex = qualities.Select((x, index) => new { index, x.Value }).OrderBy(x => x.Value).First().index;
+        else bestIndex = qualities.Select((x, index) => new { index, x.Value }).OrderByDescending(x => x.Value).First().index;
+
+        // calculate allels of current best and (if available) best known solution
+        Allele[] bestAlleles = CalculateAlleles(solutions[bestIndex]);
+        Allele[] bestKnownAlleles = null;
+        if (bestKnownSolution != null)
+          bestKnownAlleles = CalculateAlleles(bestKnownSolution);
+
+        // calculate allele frequencies
+        var frequencies = solutions.SelectMany((s, index) => CalculateAlleles(s).Select(a => new { Allele = a, Quality = qualities[index] })).
+                          GroupBy(x => x.Allele.Id).
+                          Select(x => new AlleleFrequency(x.Key,
+                                                          x.Count() / ((double)solutions.Length),
+                                                          x.Average(a => a.Allele.Impact),
+                                                          x.Average(a => a.Quality.Value),
+                                                          bestKnownAlleles == null ? false : bestKnownAlleles.Any(a => a.Id == x.Key),
+                                                          bestAlleles.Any(a => a.Id == x.Key)));
+
+        // fetch results collection
+        ResultCollection results;
+        if (!ResultsParameter.ActualValue.ContainsKey("Allele Frequency Analysis Results")) {
+          results = new ResultCollection();
+          ResultsParameter.ActualValue.Add(new Result("Allele Frequency Analysis Results", results));
+        } else {
+          results = (ResultCollection)ResultsParameter.ActualValue["Allele Frequency Analysis Results"].Value;
+        }
+
+        // store allele frequencies
+        AlleleFrequencyArray frequenciesArray = new AlleleFrequencyArray(frequencies);
+        if (!results.ContainsKey("Allele Frequencies"))
+          results.Add(new Result("Allele Frequencies", frequenciesArray));
+        else
+          results["Allele Frequencies"].Value = frequenciesArray;
+
+        // store allele frequencies history
+        if (storeHistory) {
+          if (!results.ContainsKey("Allele Frequencies History")) {
+            ItemCollection<AlleleFrequencyArray> history = new ItemCollection<AlleleFrequencyArray>();
+            history.Add(frequenciesArray);
+            results.Add(new Result("Allele Frequencies History", history));
+          } else {
+            ((ItemCollection<AlleleFrequencyArray>)results["Allele Frequencies History"].Value).Add(frequenciesArray);
+          }
+        }
+
+        // store alleles data table
+        DataTable allelesTable;
+        if (!results.ContainsKey("Alleles")) {
+          allelesTable = new DataTable("Alleles");
+          results.Add(new Result("Alleles", allelesTable));
+          allelesTable.Rows.Add(new DataRow("Unique Alleles"));
+        } else {
+          allelesTable = (DataTable)results["Alleles"].Value;
+        }
+        allelesTable.Rows["Unique Alleles"].Values.Add(frequenciesArray.Length);
       }
-
-      var frequencies = solutions.SelectMany((s, index) => CalculateAlleles(s).Select(a => new { Allele = a, Quality = qualities[index] })).
-                        GroupBy(x => x.Allele.Id).
-                        Select(x => new AlleleFrequency(x.Key,
-                                                        x.Count() / ((double)solutions.Length),
-                                                        x.Average(a => a.Allele.Impact),
-                                                        x.Average(a => a.Quality.Value),
-                                                        bestKnownAlleles == null ? false : bestKnownAlleles.Any(a => a.Id == x.Key),
-                                                        bestAlleles.Any(a => a.Id == x.Key)));
-
-      AlleleFrequencyArray frequenciesArray = new AlleleFrequencyArray(frequencies.OrderBy(x => x.AverageImpact));
-      AlleleFrequenciesParameter.ActualValue = frequenciesArray;
-      if (results.ContainsKey("Allele Frequencies"))
-        results["Allele Frequencies"].Value = frequenciesArray;
-      else
-        results.Add(new Result("Allele Frequencies", frequenciesArray));
-
       return base.Apply();
     }