gatb.core-API-0.0.0: TerminatorTemplate< Node, Edge, Graph

Interface that allows to mark certain nodes in a graph. Note: It is on the verge of becoming deprecated. More...

#include <Terminator.hpp>

Inheritance diagram for TerminatorTemplate< Node, Edge, Graph >:

Public Member Functions
	TerminatorTemplate (const Graph &graph)

virtual	~TerminatorTemplate ()

const Graph &	getGraph () const

virtual bool	isEnabled () const

virtual void	mark (Edge &edge)=0

virtual bool	is_marked (Edge &edge) const =0

virtual void	mark (Node &node)=0

virtual bool	is_marked (Node &node) const =0

virtual bool	is_marked_branching (Node &node) const =0

virtual bool	is_branching (Node &node) const =0

virtual void	reset ()=0

virtual void	dump ()=0

Public Member Functions inherited from SmartPointer
void	use ()

void	forget ()

Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()

Additional Inherited Members
Protected Member Functions inherited from SmartPointer
	SmartPointer ()

virtual	~SmartPointer ()

Detailed Description

template<typename Node, typename Edge, typename Graph>
class gatb::core::debruijn::impl::TerminatorTemplate< Node, Edge, Graph >

Interface that allows to mark certain nodes in a graph. Note: It is on the verge of becoming deprecated.

In short: don't use it. Use the MPHF.

This is a legacy class that was used when the graph did not have a MPHF. I.e. in Minia version 1. Back then, it was not possible to directly tag nodes inside the graph structure. So this Terminator class uses an external data structure to mark some of the nodes (specifically, the branching nodes). It was used during graph traversal for instance.

The Terminator interface provides such a service. It is often used by the Traversal class during its traversing process.

The name Terminator is just related to termination, we needed a way to ensure that we don't traverse the same contig twice, so that the algorithm terminates eventually.

Constructor & Destructor Documentation

TerminatorTemplate ( const Graph & graph )

inline

Constructor

Parameters

[in] graph : the graph

virtual ~TerminatorTemplate ( )

inlinevirtual

Destructor.

Member Function Documentation

virtual void dump ( )

pure virtual

Dump (for debug purpose).

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

const Graph& getGraph ( ) const

inline

Get the graph.

Returns: the graph.

virtual bool is_branching ( Node & node ) const

pure virtual

Tells whether a node is branching

Parameters

[in] node : node to be checked

Returns: true if the node is branching, false otherwise.

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

virtual bool is_marked ( Edge & edge ) const

pure virtual

Tells whether an edge is marked

Parameters

[in] edge : edge to be checked

Returns: true if the edge is marked, false otherwise

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

virtual bool is_marked ( Node & node ) const

pure virtual

Tells whether a node is marked

Parameters

[in] node : node to be checked

Returns: true if the node is marked, false otherwise

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

virtual bool is_marked_branching ( Node & node ) const

pure virtual

Tells whether a branching node is marked

Parameters

[in] node : node to be checked

Returns: true if the node is marked, false otherwise

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

virtual bool isEnabled ( ) const

inlinevirtual

Tells whether marking nodes is allowed or not

Returns: true if marking nodes is allowed, false otherwise.

Reimplemented in NullTerminatorTemplate< Node, Edge, Graph >.

virtual void mark ( Edge & edge )

pure virtual

Mark the provided edge

Parameters

[in] edge : edge to be marked.

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

virtual void mark ( Node & node )

pure virtual

Mark the provided node.

Parameters

[in] node : node to be marked.

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

virtual void reset ( )

pure virtual

Reset the current marked nodes/edges.

Implemented in MPHFTerminatorTemplate< Node, Edge, Graph >, BranchingTerminatorTemplate< Node, Edge, Graph >, and NullTerminatorTemplate< Node, Edge, Graph >.

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

/builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/debruijn/impl/Terminator.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

template<typename Node, typename Edge, typename Graph> class gatb::core::debruijn::impl::TerminatorTemplate< Node, Edge, Graph >

Constructor & Destructor Documentation

Member Function Documentation

template<typename Node, typename Edge, typename Graph>
class gatb::core::debruijn::impl::TerminatorTemplate< Node, Edge, Graph >