vg::ZipCodeTree::reverse_iterator Class Reference

#include <zip_code_tree.hpp>

Public Types
enum	State {   S_START, S_SCAN_CHAIN, S_STACK_SNARL, S_SCAN_SNARL,   S_SKIP_CHAIN }

Public Member Functions
	reverse_iterator (vector< tree_item_t >::const_reverse_iterator rbegin, vector< tree_item_t >::const_reverse_iterator rend, size_t distance_limit=std::numeric_limits< size_t >::max())
	reverse_iterator (const reverse_iterator &other)
	reverse_iterator (reverse_iterator &&other)
reverse_iterator &	operator= (const reverse_iterator &other)
reverse_iterator &	operator= (reverse_iterator &&other)
reverse_iterator &	operator++ ()
	Move left. More...
bool	operator== (const reverse_iterator &other) const
	Compare for equality to see if we hit end (the past-the-left position) More...
bool	operator!= (const reverse_iterator &other) const
	Compare for inequality. More...
seed_result_t	operator* () const
	Get the index and orientation of the seed we are currently at, and the distance to it. More...

Private Member Functions
std::stack< size_t > &	stack ()
	Accessor to lazily initialize a stack for the iterator. More...
void	push (size_t value)
	Push a value to the stack. More...
size_t	pop ()
	Pop a value from the stack and return it. More...
size_t &	top ()
	Get a mutable reference to the value on top of the stack. More...
void	dup ()
	Duplicate the top item on the stack. More...
size_t	depth () const
	Check stack depth. More...
void	swap ()
	Reverse the top two elements of the stack. More...
void	state (State new_state)
	Adopt a new state. More...
void	halt ()
bool	tick ()

Private Attributes
vector< tree_item_t >::const_reverse_iterator	it
	Where we are in the stored tree. More...
vector< tree_item_t >::const_reverse_iterator	rend
	Where the rend is where we have to stop. More...
size_t	distance_limit
	Distance limit we will go up to. More...
std::unique_ptr< std::stack< size_t > >	stack_data
State	current_state
	Current state of the automaton. More...

Detailed Description

Iterator that looks left in the tree from a seed, possibly up to a maximum base distance.

See https://github.com/benedictpaten/long_read_giraffe_chainer_prototype/blob/b590c34055474b0c901a681a1aa99f1651abb6a4/zip_tree_iterator.py.

Member Enumeration Documentation

State

enum vg::ZipCodeTree::reverse_iterator::State

Type for the state of the I-can't-believe-it's-not-a-pushdown-automaton

Enumerator
S_START
S_SCAN_CHAIN
S_STACK_SNARL
S_SCAN_SNARL
S_SKIP_CHAIN

Constructor & Destructor Documentation

reverse_iterator() [1/3]

vg::ZipCodeTree::reverse_iterator::reverse_iterator	(	vector< tree_item_t >::const_reverse_iterator	rbegin,
		vector< tree_item_t >::const_reverse_iterator	rend,
		size_t	distance_limit = std::numeric_limits<size_t>::max()
	)

Make a reverse iterator wrapping the given reverse iterator, until the given rend, with the given distance limit.

reverse_iterator() [2/3]

vg::ZipCodeTree::reverse_iterator::reverse_iterator

(

const reverse_iterator &

other

)

reverse_iterator() [3/3]

vg::ZipCodeTree::reverse_iterator::reverse_iterator

(

reverse_iterator &&

other

)

Member Function Documentation

depth()

auto vg::ZipCodeTree::reverse_iterator::depth ( ) const

private

Check stack depth.

dup()

auto vg::ZipCodeTree::reverse_iterator::dup ( )

private

Duplicate the top item on the stack.

halt()

auto vg::ZipCodeTree::reverse_iterator::halt ( )

private

Stop parsing because nothing else can be below the distance limit. This moves the current iterator it.

operator!=()

bool vg::ZipCodeTree::reverse_iterator::operator!= ( const reverse_iterator &  other ) const

inline

Compare for inequality.

operator*()

auto vg::ZipCodeTree::reverse_iterator::operator*

(

)

const

Get the index and orientation of the seed we are currently at, and the distance to it.

operator++()

auto vg::ZipCodeTree::reverse_iterator::operator++

(

)

Move left.

operator=() [1/2]

auto vg::ZipCodeTree::reverse_iterator::operator=

(

const reverse_iterator &

other

)

operator=() [2/2]

auto vg::ZipCodeTree::reverse_iterator::operator=

(

reverse_iterator &&

other

)

operator==()

auto vg::ZipCodeTree::reverse_iterator::operator==

(

const reverse_iterator &

other

)

const

Compare for equality to see if we hit end (the past-the-left position)

pop()

auto vg::ZipCodeTree::reverse_iterator::pop ( )

private

Pop a value from the stack and return it.

push()

auto vg::ZipCodeTree::reverse_iterator::push ( size_t  value )

private

Push a value to the stack.

stack()

std::stack<size_t>& vg::ZipCodeTree::reverse_iterator::stack ( )

inlineprivate

Accessor to lazily initialize a stack for the iterator.

state()

auto vg::ZipCodeTree::reverse_iterator::state ( State  new_state )

private

Adopt a new state.

swap()

auto vg::ZipCodeTree::reverse_iterator::swap ( )

private

Reverse the top two elements of the stack.

tick()

auto vg::ZipCodeTree::reverse_iterator::tick ( )

private

Tick the automaton, looking at the symbol at *it and updating the stack and current_state. Returns true to yield a value at the current symbol, or to halt, and false otherwise.

top()

auto vg::ZipCodeTree::reverse_iterator::top ( )

private

Get a mutable reference to the value on top of the stack.

Member Data Documentation

current_state

State vg::ZipCodeTree::reverse_iterator::current_state

private

Current state of the automaton.

distance_limit

size_t vg::ZipCodeTree::reverse_iterator::distance_limit

private

Distance limit we will go up to.

it

vector<tree_item_t>::const_reverse_iterator vg::ZipCodeTree::reverse_iterator::it

private

Where we are in the stored tree.

rend

vector<tree_item_t>::const_reverse_iterator vg::ZipCodeTree::reverse_iterator::rend

private

Where the rend is where we have to stop.

stack_data

std::unique_ptr<std::stack<size_t> > vg::ZipCodeTree::reverse_iterator::stack_data

private

Stack for computing distances. Not allocated unless we actually go to use it, so rend() deosn't need to carry one.

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The documentation for this class was generated from the following files:

• src/zip_code_tree.hpp
• src/zip_code_tree.cpp