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Add metadata information record #131

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Boarders opened this issue Apr 8, 2019 · 0 comments
Open

Add metadata information record #131

Boarders opened this issue Apr 8, 2019 · 0 comments

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@Boarders
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Boarders commented Apr 8, 2019

The types of phylogenetic graphs we use are described in Bio.Graph.Constructions inside pcg-data-structures. For example a FinalDecorationDAG is described as:

type FinalDecorationDAG =
       PhylogeneticDAG
         (TraversalTopology, Double, Double, Double, Data.Vector.Vector (NonEmpty TraversalFocusEdge))
         EdgeAnnotation
         NodeLabel
         (ContinuousOptimizationDecoration ContinuousCharacter)
         (FitchOptimizationDecoration          StaticCharacter)
         (AdditiveOptimizationDecoration       StaticCharacter)
         (SankoffOptimizationDecoration        StaticCharacter)
         (SankoffOptimizationDecoration        StaticCharacter)
         (DynamicDecorationDirectOptimization DynamicCharacter)

The first field here (TraversalTopology, Double, Double, Double, Data.Vector.Vector (NonEmpty TraversalFocusEdge)) corresponds to data that is stored in the metadata sequence. I think it would be better if this were re-written as a record as it is unclear what the various parts of the tuples mean without going to look it up.

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