lib5c.operators.base module

class lib5c.operators.base.InteractionMatrixOperator

Bases: object

Abstract base class for objects that operate on single InteractionMatrix objects.

Subclasses should implement an apply_inplace() function that takes in an InteractionMatrix object and returns an InteractionMatrix object but is allowed to operate in-place. Additional parameters requried by the apply_inplace() function can be either passed to the function as **kwargs or stored in properties of the InteractionMatrixOperator subclass.

apply(target, **kwargs)

Apply this operator to a target InteractionMatrix, returning a copy.

Parameters

• target (InteractionMatrix) – The InteractionMatrix object to operate on.

• kwargs (other keyword arguments) – To be utilized by subclasses.

Returns

The result of applying the operation.

Return type

InteractionMatrix

apply_by_region(target, **kwargs)

Apply this operator independently to each region of a target InteractionMatrix.

Parameters

• target (InteractionMatrix) – The InteractionMatrix object to operate on.

• kwargs (other keyword arguments) – To be utilized by subclasses.

Returns

The result of applying the operation.

Return type

InteractionMatrix

Notes

To support logging, we used the following pattern:

1. Log on the target object to indicate regional application

2. Maintain a list of results of the application

3. Instantiate

4. Get the first result from the list and copy its log to the instance

5. Log on the result object to indicate end of regional application

6. Return the instance

If you see 'applying by region' with no closing 'done applying by region', that indictates that you are looking at a target object for an apply-by-region operation that was not done in-place. Such a log line can be ignored.

If you see 'applying by region' with a closing 'done applying by region', that indicates that you are looking at a result object for an apply-by-region operation that was not done in-place. The lines in the block show the log for only the first region, but each region was processed identically.

apply_inplace(target, **kwargs)

Apply this operator to a target InteractionMatrix in-place.

Parameters

• target (InteractionMatrix) – The InteractionMatrix object to operate on.

• kwargs (other keyword arguments) – To be utilized by subclasses.

Returns

The result of applying the operation.

Return type

InteractionMatrix

class lib5c.operators.base.MultiInteractionMatrixOperator

Bases: object

Abstract base class for objects that operate on multiple InteractionMatrix objects.

Subclasses should implement an apply_inplace() function that takes in an list of InteractionMatrix objects and returns a list of InteractionMatrix objects but is allowed to operate in-place. Additional parameters requried by the apply_inplace() function can be either passed to the function as **kwargs or stored in properties of the MultiInteractionMatrixOperator subclass.

apply(targets, **kwargs)

Apply this operator to a list of target InteractionMatrix objects.

Parameters

• targets (list of InteractionMatrix) – The list of InteractionMatrix objects to operate on simultaneously.

• kwargs (other keyword arguments) – To be utilized by subclasses.

Returns

The result of applying the operation.

Return type

list of InteractionMatrix

apply_by_region(targets, **kwargs)

Apply this operator independently to each region of the target InteractionMatrix objects.

Parameters

• targets (list of InteractionMatrix) – The list of InteractionMatrix objects to operate on simultaneously.

• kwargs (other keyword arguments) – To be utilized by subclasses.

Returns

The result of applying the operation.

Return type

list of InteractionMatrix

Notes

To support logging, we used the following pattern:

1. Log on all target objects to indicate regional application

2. Maintain a dict of list of results of the application

3. Instantiate the results

4. Get the first region of the first result from the dict of lists and copy its log to each instance

5. Log on all result objects to indicate end of regional application

6. Return the instances

If you see 'applying by region' with no closing 'done applying by region', that indictates that you are looking at a target object for an apply-by-region operation that was not done in-place. Such a log line can be ignored.

If you see 'applying by region' with a closing 'done applying by region', that indicates that you are looking at a result object for an apply-by-region operation that was not done in-place. The lines in the block show the log for only the first region, but each region was processed identically.

apply_inplace(targets, **kwargs)

Apply this operator to a target InteractionMatrix in-place.

Parameters

• targets (list of InteractionMatrix) – The list of InteractionMatrix objects to operate on simultaneously.

• kwargs (other keyword arguments) – To be utilized by subclasses.

Returns

The result of applying the operation.

Return type

list of InteractionMatrix