jdna.linked_list¶

Linked list model to represent linear or circular sequences.

Classes

`DoubleLinkedList`([data, first, cyclic])	A generic double linked list class.
`EmptyNode`()	Node constructor.
`LinkedListMatch`(template_bounds, …)	A match object.
`Node`(data)	A node in a linked list.

Exceptions

`LinkedListException`	Generic linked list exception.
`LinkedListIndexError`	Indices were out of bounds for LinkedList.

class jdna.linked_list.DoubleLinkedList(data: Sequence[Any] = None, first: jdna.linked_list.Node = None, cyclic: bool = False)[source]¶

Bases: object

A generic double linked list class.

linked list construction.

Parameters

data (iterable) – iterable data
first (Node) – first node

class Direction[source]¶

Bases: enum.IntFlag

An enumeration.

NODE_CLASS¶: alias of Node

property circular¶: Alias for cyclic.

static collect_nodes(nodes)[source]¶

Return all visisted nodes and return an unordered set of nodes.

Returns: all visited nodes
Return type: set

compare(other: jdna.linked_list.DoubleLinkedList) → bool[source]¶

Compares two linked lists. If both are cyclic, will attempt to reindex.

Parameters: other (DoubleLinkedList) – other linked list
Returns: whether sequence data is equivalent
Return type: bool

copy_slice(start: jdna.linked_list.Node, end: jdna.linked_list.Node) → jdna.linked_list.DoubleLinkedList[source]¶

Return a copy of the sequence between ‘start’ and ‘end’ nodes.

If start is None, return the slice copy from head to end. If end is None, return copy from start to tail. If both start and end are None return None.

static find_ends(nodes)[source]¶: Efficiently finds the head and tails from a group of nodes.

find_iter(query: jdna.linked_list.DoubleLinkedList, min_query_length: int = None, direction: int = <Direction.FORWARD: 1>, protocol: Callable = None, depth: int = None)[source]¶

Iteratively finds positions that match the query.

Parameters

query (DoubleLinkedList) – query list to find
min_query_length (inst) – the minimum number of matches to return. If None, find_iter will only return complete matches
direction (int or tuple) – If Direction.FORWARD (+1), find iter will search from the query head and search forward, potentially leaving a ‘tail’ overhang on the query. If Direction.REVERSE (-1), find iter will search from the query tail and search reverse, potentially leaving a ‘head’ overhang on the query. If a tuple, the template_direction and query_direction are set respectively.
protocol (callable) – the callable taking two parameters (as Node) to compare during find. If None, defaults to ‘equivalent’

Returns

list of LinkedListMatches

Return type

list

inclusive_range(i: int, j: int) → Generator[jdna.linked_list.Node, None, None][source]¶

Return generator for inclusive nodes between index i and j.

If i is None, assume i is the head node.

classmethod new_slice(start: jdna.linked_list.Node, end: jdna.linked_list.Node) → jdna.linked_list.DoubleLinkedList[source]¶: Return a copy of the sequence between ‘start’ and ‘end’ nodes)

node_range(start: jdna.linked_list.Node, end: jdna.linked_list.Node) → Generator[jdna.linked_list.Node, None, None][source]¶: Iterate between ‘start’ to ‘end’ nodes (inclusive)

range(i: int, j: int) → Generator[jdna.linked_list.Node, None, None][source]¶: Returns an iterator from node at ‘i’ to node at ‘j-1’.

class jdna.linked_list.EmptyNode[source]¶

Bases: jdna.linked_list.Node

Node constructor. Stores a single piece of data.

Parameters: data (any) – data

_break_connections()¶

Break connections in this node.

Returns
Return type

_complete_match(node: jdna.linked_list.Node, next_method: Callable) → bool¶

Return whether the longest match between two nodes is equivalent.

Parameters

node (Node) – the node to compare
next_method (callable) – how to obtain the next node

Returns

whether the longest match between two nodes is equivalent

Return type

bool

add_next(data)¶

Create a new node and add to next.

Parameters: data (any) – any data
Returns: the new node
Return type: Node

add_prev(data)¶

Create a new node and add to previous.

Parameters: data (any) – any data
Returns: the new node
Return type: Node

cut_next()¶

Cut the next node, return the cut node.

Returns: the cut (next) node
Return type: Node

cut_prev()¶

Cut the previous node, return the cut node.

Returns: the cut (previous) node
Return type: Node

equivalent(other: jdna.linked_list.Node) → bool¶: Evaluates whether two nodes hold the same data.

find_first() → jdna.linked_list.Node¶

Find the head node.

Returns
Return type

find_last() → jdna.linked_list.Node¶

Find the tail node.

Returns
Return type

fwd(stop_node: Optional[jdna.linked_list.Node] = None, stop_criteria: Callable = None) → Generator¶

Propogates forwards until stop node is visited or stop criteria is reached.

Parameters

stop_node –
stop_criteria –

Returns

Return type

longest_match(node: jdna.linked_list.Node, next_method: Callable = None) → Tuple[jdna.linked_list.Node, jdna.linked_list.Node]¶

Find the longest match between two linked_lists.

Parameters

node (Node) – the node to compare
next_method (callable) – how to obtain the next node

Returns

list of tuples containing matching nodes

Return type

list

next()¶

Return the next node.

Returns: the next node
Return type: Node

prev()¶

Return the previous node.

Returns: the previous node
Return type: Node

remove()¶

Remove node from linked list, connecting the previous and next nodes together.

Returns: None
Return type: None

rev(stop_node: Optional[jdna.linked_list.Node] = None, stop_criteria: Callable = None) → Generator[jdna.linked_list.Node, None, None]¶

Propogates backwards until stop node is visited or stop criteria is reached.

Parameters

stop_node –
stop_criteria –

Returns

Return type

set_next(node: jdna.linked_list.Node)¶

Set the next node.

Parameters: node –
Returns
Return type

set_prev(node: jdna.linked_list.Node)¶

Set the previous node.

Parameters: node –
Returns
Return type

swap()¶

Swap the previous and next nodes.

Returns: None
Return type: None

exception jdna.linked_list.LinkedListException[source]¶

Bases: Exception

Generic linked list exception.

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception jdna.linked_list.LinkedListIndexError[source]¶

Bases: jdna.linked_list.LinkedListException, IndexError

Indices were out of bounds for LinkedList.

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class jdna.linked_list.LinkedListMatch(template_bounds: Tuple[jdna.linked_list.Node, jdna.linked_list.Node], query_bounds: Tuple[jdna.linked_list.Node, jdna.linked_list.Node], template: jdna.linked_list.DoubleLinkedList, query: jdna.linked_list.DoubleLinkedList)[source]¶

Bases: object

A match object.

classmethod batch_create(template_bounds_list: List[Tuple[jdna.linked_list.Node, jdna.linked_list.Node]], query_bounds_list: List[Tuple[jdna.linked_list.Node, jdna.linked_list.Node]], template: jdna.linked_list.DoubleLinkedList, query: jdna.linked_list.DoubleLinkedList) → List[jdna.linked_list.LinkedListMatch][source]¶

Efficiently create several LinkedListMatches from lists of template starts/ends and query starts/ends.

Parameters

template_bounds_list (template DoubleLinkedList) – list of 2 len tuples containing starts and ends from a template
query_bounds_list (query DoubleLinkedList) – list of 2 len tuples containing starts and ends from a query
template (DoubleLinkedList) – the template
query (DoubleLinkedList) – the query

Returns

matchese

Return type

list of LinkedListMatch

class jdna.linked_list.Node(data)[source]¶

Bases: object

A node in a linked list.

Node constructor. Stores a single piece of data.

Parameters: data (any) – data

_break_connections()[source]¶

Break connections in this node.

Returns
Return type

_complete_match(node: jdna.linked_list.Node, next_method: Callable) → bool[source]¶

Return whether the longest match between two nodes is equivalent.

Parameters

node (Node) – the node to compare
next_method (callable) – how to obtain the next node

Returns

whether the longest match between two nodes is equivalent

Return type

bool

add_next(data)[source]¶

Create a new node and add to next.

Parameters: data (any) – any data
Returns: the new node
Return type: Node

add_prev(data)[source]¶

Create a new node and add to previous.

Parameters: data (any) – any data
Returns: the new node
Return type: Node

cut_next()[source]¶

Cut the next node, return the cut node.

Returns: the cut (next) node
Return type: Node

cut_prev()[source]¶

Cut the previous node, return the cut node.

Returns: the cut (previous) node
Return type: Node

equivalent(other: jdna.linked_list.Node) → bool[source]¶: Evaluates whether two nodes hold the same data.

find_first() → jdna.linked_list.Node[source]¶

Find the head node.

Returns
Return type

find_last() → jdna.linked_list.Node[source]¶

Find the tail node.

Returns
Return type

fwd(stop_node: Optional[jdna.linked_list.Node] = None, stop_criteria: Callable = None) → Generator[source]¶

Propogates forwards until stop node is visited or stop criteria is reached.

Parameters

stop_node –
stop_criteria –

Returns

Return type

longest_match(node: jdna.linked_list.Node, next_method: Callable = None) → Tuple[jdna.linked_list.Node, jdna.linked_list.Node][source]¶

Find the longest match between two linked_lists.

Parameters

node (Node) – the node to compare
next_method (callable) – how to obtain the next node

Returns

list of tuples containing matching nodes

Return type

list

next()[source]¶

Return the next node.

Returns: the next node
Return type: Node

prev()[source]¶

Return the previous node.

Returns: the previous node
Return type: Node

remove()[source]¶

Remove node from linked list, connecting the previous and next nodes together.

Returns: None
Return type: None

rev(stop_node: Optional[jdna.linked_list.Node] = None, stop_criteria: Callable = None) → Generator[jdna.linked_list.Node, None, None][source]¶

Propogates backwards until stop node is visited or stop criteria is reached.

Parameters

stop_node –
stop_criteria –

Returns

Return type

set_next(node: jdna.linked_list.Node)[source]¶

Set the next node.

Parameters: node –
Returns
Return type

set_prev(node: jdna.linked_list.Node)[source]¶

Set the previous node.

Parameters: node –
Returns
Return type

swap()[source]¶

Swap the previous and next nodes.

Returns: None
Return type: None

jdna

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jdna.linked_list¶