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High-level description

The LeafSubsampler class in LeafSubsampler.py defines an abstract base class for all leaf samplers in the Cassiopeia library. It provides a blueprint for creating derived classes that implement different methods for subsampling the leaves of a CassiopeiaTree.

Leaf subsampling is a common operation in phylogenetic analysis, where a subset of leaves (representing cells or taxa) is selected from a larger tree to perform downstream analyses. This can be useful for reducing computational complexity, focusing on specific lineages, or simulating different sampling scenarios.

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Code Structure

This code defines an abstract base class LeafSubsampler with one abstract method subsample_leaves. This method is meant to be implemented by concrete leaf subsampler classes that inherit from this base class.

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References

This code references the following symbols from other files:

  • cassiopeia.data.CassiopeiaTree: This class represents a phylogenetic tree with associated data, such as character states and metadata.
  • cassiopeia.mixins.LeafSubsamplerError: This exception class is raised for errors specific to leaf subsampling operations.
  • cassiopeia.mixins.LeafSubsamplerWarning: This warning class is used to issue warnings related to leaf subsampling.
  • abc.ABC and abc.abstractmethod: These are used to define abstract base classes and methods, ensuring that derived classes implement the required functionality.

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Symbols

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LeafSubsampler

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Description

This is an abstract base class for all leaf samplers. It defines the interface that concrete leaf sampler classes must implement.

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Inputs

This class does not have an __init__ method and therefore does not take any inputs.

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Outputs

This class does not directly return any outputs.

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Internal Logic

This class does not have any internal logic as it is an abstract base class.

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Side Effects

This class does not have any side effects as it is an abstract base class.