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# CassiopeiaSolver.py

## High-level description

The `CassiopeiaSolver` is an abstract base class for all phylogenetic inference algorithms in the Cassiopeia framework. It defines the basic structure and interface for solvers, requiring subclasses to implement the `solve` method, which performs the actual tree inference. It also handles the transformation of prior probabilities into weights used by some solvers.

## Code Structure

The `CassiopeiaSolver` class is an abstract base class. It doesn't have any internal logic or complex interactions between symbols. The main purpose of this class is to define a common interface for all derived solver classes.

## Symbols

### `CassiopeiaSolver`

#### Description

This is an abstract base class for all phylogenetic inference algorithms. It defines the basic structure and interface for solvers.

#### Inputs

| Name                  | Type | Description                                                                                                             |
| :-------------------- | :--- | :---------------------------------------------------------------------------------------------------------------------- |
| prior\_transformation | str  | A string specifying the function to use for transforming prior probabilities into weights. Defaults to "negative\_log". |

#### Outputs

This class does not have any outputs.

#### Internal Logic

This class does not have any internal logic.

### `solve`

#### Description

This is an abstract method that needs to be implemented by all derived solver classes. It performs the actual tree inference.

#### Inputs

| Name                          | Type           | Description                                                                                                                                                 |
| :---------------------------- | :------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------- |
| cassiopeia\_tree              | CassiopeiaTree | A `CassiopeiaTree` object storing character information for phylogenetic inference.                                                                         |
| layer                         | Optional\[str] | Layer storing the character matrix for solving. If None, the default character matrix is used in the `CassiopeiaTree`.                                      |
| collapse\_mutationless\_edges | bool           | Indicates if the final reconstructed tree should collapse mutationless edges based on internal states inferred by Camin-Sokal parsimony. Defaults to False. |
| logfile                       | str            | File location to log output. Defaults to "stdout.log".                                                                                                      |

#### Outputs

This method does not have any outputs. It modifies the input `cassiopeia_tree` object by populating its tree attribute.

#### Internal Logic

This method is abstract and does not have any internal logic. It needs to be implemented by derived classes.