DataSimulator.py

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High-level description

The DataSimulator class in cassiopeia/simulator/DataSimulator.py is an abstract base class for simulating various types of data to overlay onto a CassiopeiaTree. This class provides a blueprint for creating simulators that can generate data like lineage tracing information, transcriptomes, or proteomes, allowing for in silico exploration of different data types and their impact on phylogenetic reconstruction.

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Code Structure

This code defines a single abstract class DataSimulator which serves as a template for concrete data simulator implementations. It doesn’t have complex interconnections between symbols.

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Symbols

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Symbol Name: DataSimulator

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Description

This abstract class defines the blueprint for all data simulators. It mandates that any derived class must implement the overlay_data method.

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Inputs

This class doesn’t take any input during initialization.

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Outputs

This class doesn’t return any output during initialization.

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Internal Logic

This class doesn’t have any internal logic as it’s an abstract class.

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Symbol Name: overlay_data

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Description

This abstract method defines the core functionality of a DataSimulator. It’s intended to be implemented by derived classes to overlay specific types of data onto a CassiopeiaTree.

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Inputs

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Outputs

This method doesn’t return any value. It modifies the input CassiopeiaTree in-place.

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Internal Logic

This method is abstract and doesn’t have an implementation in this base class. Derived classes are responsible for implementing the specific logic for data overlay.