Evolutionary tracking of solutions within GP

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In other to perform theoretical investigations on building blocks and bloat, some new functionality is required:

• complete genealogical trees of solution candidates
• analyze evolutionary operators and search trajectories

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r7479: Implemented an initial set of features: individual ancestry, genealogy tracking via customized genetic operators and data structures.

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r7513: Cleaned up unneeded folders
r7514: Merged latest trunk changes to SymbolicExpressionTreeEncoding.
r7515: Added tracking for mutation operators.

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r7522: Merged changes from trunk, rigged the TournamentSelector to track clones, improved tracking code and genealogy graph layout.

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r7779: Implemented new View, improved functionality (tracking of fragments and operators)

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r7785: Moved tree matching functionality in separate class, implemented new tree fragments analyzer. Fixed bug in GetCutIndex method.

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r7788: Fixed bug in fragment tracing.

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r7792:

• Removed GetCutIndex method, and corresponding index field in the GenealogyGraphNode.
• Implemented tracking for mutated fragments.
• Improved FindMatch method.
• Added IterateNodesBreadth functionality to symbolic expression trees and nodes.
• Added check conditions for clearing global tracking structures so that the 2 analyzers are not mutually exclusive anymore.

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r7800: Fixed display of genetic fragments (received via crossover) in the GenealogyGraphView. Added parent, offspring and fragment lengths histogram.

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r7817: Fixed a small bug in the TracingSymbolicExpressionTreeCrossover. Fixed bug in fragment matching code.

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r7997: New analyzer: SymbolicExpressionTreeRelativeLengthAnalyzer. Rewrote the SymbolicExpressionTreeFragmentsAnalyzer, added generic wrapper to wrap HL objects as items.

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r8213: Performance improvements for the GenealogyGraph. Minor refactoring to VisualGenealogyGraphArc and VisualGenealogyGraphNode classes. Added new functionality to the SymbolicExpressionTreeFragmentsAnalyzer, minor refactoring in the other two analyzers. Refactored View code. Updated project references and plugin dependencies and added HeuristicLab.Problems.DataAnalysis.Symbolic to the branch.

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r8236: Refactored code in the GenealogyGraphChart and the SymbolicExpressionTreeGenealogyAnalyzer. Used gradient from HeuristicLab.Common to color the graph nodes.

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r8248: Separated instance-specific attributes of graph node objects from the generic genealogy graph, into metadata objects kept by the specific graph class which corresponds to the specific problem instance (so for instance the SymbolicExpressionTreeGenealogyGraph will keep info about node ranks and qualities etc because that info is specific to symbolic data analysis problems).

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r8249: Fixed small bug (correct counting of node ranks) in the SymbolicExpressionTreeGenealogyAnalyzer. Fixed node tool tips in the GenealogyGraphChart.

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r8555: Partial commit -- Introduced more specific graph class for symbolic expression problems.

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r8556: Partial commit -- Modified genealogy graph chart and view to reflect changes in the class hierarchy.

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r8557: Introduced base class and interface for tracing operators. Introduced SymbolicExpressionTreeNodeComparer interface to be implemented by node matching operators. Fixed bug in the TracingSymbolicExpressionTreeManipulator where nodes modified by the Full- and OnePoint tree shakers were not correctly detected. The SymbolicExpressionTreeNodeSimilarityComparer is now injected in the tracing genetic operators as a parameter.

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r9082: Renamed and refactored genealogy graph components. Added SymbolGraph and FPGraph (frequent pattern graph). Added evolvability and genetic operator average improvement analyzer.

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r9083: Merged HeuristicLab.Encodings.SymbolicExpressionTreeEncoding from trunk. Added Fragment class implementing IFragment interface.

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r9084: HeuristicLab.EvolutionaryTracking.Views: refactored the GenealogyGraphChart and the GenealogyGraphView. Fixed lineage display bug.

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r9237: Merged HeuristicLab.Encodings.SymbolicExpressionTreeEncoding trunk changes into the branch. Changed fragments using the tree manipulator are now tracked using the SymbolicExpressionTreeNodeComparer.

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r9238: Added base class for the fragment analyzers. Improved analyzers, added SymbolicExpressionTreeRelativeFragmentDepthAnalyzer. Added LineageExplorer.

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r9239: Minor updates to existing views. Added LineageExplorerView.

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r9241: Merged trunk changes for HeuristicLab.Problems.DataAnalysis.Symbolic. Added SymbolicDataAnalysisSolutionTextRenderer, a class for displaying symbolic expression trees in the console.

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r9246: Removed commented code from TracingSymbolicExpressionTreeManipulator.cs. Updated project file.

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r9247: Fixed serialization bug of DirectedGraph/Vertex.cs. Modifier behavior of the SymbolicExpressionTreeGenealogyGraphBuilder so that now instances of an elite individual are connected in the graph, which makes it easier to deal with lineages.

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r9248: Added Analyzers/SymbolicExpressionTreeEvolvabilityAnalyzer.cs.

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r9249: Updated matching criteria to BoolValues in SymbolicDataAnalysisExpressionTreeMatching.cs.

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r9250: Updated LineageExplorerView and added functionality for highlighting common fragments in a given tree. Fixed view layout and element anchoring.

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r9293: Added new similarity measures and moved them to separate class SymbolicDataAnalysisExpressionTreeSimilarity.cs.

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r9296: Updated analyzers.

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r9416: Fixed serialization of genetic fragments, added interface ISymbolicExpressionTreeNodeSimilarityComparer

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r9419: Refactoring of directed graph components, added code for correctly serializing vertices and edges. Added specific building blocks analyzers and new population diversity analyzer which correctly integrates with the parallel engine.

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r9420: Improved the LineageExplorerView, added generation labels in the GenealogyGraphChart, added new visual component VisualGenealogyGraphTextLabel.

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r9421: Merged trunk changes for HeuristicLab.Optimization.Views.

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r9423: Implemented GeneticItem-based similarity measure. Renamed ISymbolicExpressionTreeNodeComparer to ISymbolicExpressionTreeNodeSimilarityComparer.

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r9424: Merged HeuristicLab.Selection.