AlignerNaive

class AlignerNaive(strategy='start-end')[source]

Naive strategies for multiple alignment.

Naive strategies supported by this estimator are:

start: aligns starts (lowest index), does no squeezing/stretching
end: aligns ends (highest index), no squeezing/stretching
start-end: aligns starts and ends, stretches linearly and rounds

Parameters:

strategy: str, one of “start”, “end”, “start-end” (default): start: aligns starts (lowest index), does no squeezing/stretching end: aligns ends (highest index), no squeezing/stretching start-end: aligns starts and ends, stretches linearly and rounds

Attributes:

is_fitted: Whether fit has been called.

Methods

`check_is_fitted`([method_name])	Check if the estimator has been fitted.
`clone`()	Obtain a clone of the object with same hyper-parameters and config.
`clone_tags`(estimator[, tag_names])	Clone tags from another object as dynamic override.
`create_test_instance`([parameter_set])	Construct an instance of the class, using first test parameter set.
`create_test_instances_and_names`([parameter_set])	Create list of all test instances and a list of names for them.
`fit`(X[, Z])	Fit alignment given series/sequences to align.
`get_aligned`()	Return aligned version of sequences passed to fit.
`get_alignment`()	Return alignment for sequences/series passed in fit (iloc indices).
`get_alignment_loc`()	Return alignment for sequences/series passed in fit (loc indices).
`get_class_tag`(tag_name[, tag_value_default])	Get class tag value from class, with tag level inheritance from parents.
`get_class_tags`()	Get class tags from class, with tag level inheritance from parent classes.
`get_config`()	Get config flags for self.
`get_distance`()	Return overall distance of alignment.
`get_distance_matrix`()	Return distance matrix of alignment.
`get_fitted_params`([deep])	Get fitted parameters.
`get_param_defaults`()	Get object's parameter defaults.
`get_param_names`([sort])	Get object's parameter names.
`get_params`([deep])	Get a dict of parameters values for this object.
`get_tag`(tag_name[, tag_value_default, ...])	Get tag value from instance, with tag level inheritance and overrides.
`get_tags`()	Get tags from instance, with tag level inheritance and overrides.
`get_test_params`([parameter_set])	Return testing parameter settings for the estimator.
`is_composite`()	Check if the object is composed of other BaseObjects.
`load_from_path`(serial)	Load object from file location.
`load_from_serial`(serial)	Load object from serialized memory container.
`reset`()	Reset the object to a clean post-init state.
`save`([path, serialization_format])	Save serialized self to bytes-like object or to (.zip) file.
`set_config`(**config_dict)	Set config flags to given values.
`set_params`(**params)	Set the parameters of this object.
`set_random_state`([random_state, deep, ...])	Set random_state pseudo-random seed parameters for self.
`set_tags`(**tag_dict)	Set instance level tag overrides to given values.