gatb.core-API-0.0.0
Public Member Functions | Static Public Member Functions | List of all members
UnitigsConstructionAlgorithm< span > Class Template Reference

Computation of the unitigs of a Graph, using BCALM 2. More...

#include <UnitigsConstructionAlgorithm.hpp>

Inheritance diagram for UnitigsConstructionAlgorithm< span >:
Inheritance graph

Public Member Functions

 UnitigsConstructionAlgorithm (tools::storage::impl::Storage &storage, std::string unitigs_filename, size_t nb_cores=0, tools::misc::IProperties *options=0, bool do_bcalm=true, bool do_bglue=true, bool do_links=true)
 
 ~UnitigsConstructionAlgorithm ()
 
void execute ()
 
- Public Member Functions inherited from Algorithm
 Algorithm (const std::string &name, int nbCores=-1, gatb::core::tools::misc::IProperties *input=0)
 
virtual ~Algorithm ()
 
std::string getName () const
 
void run ()
 
virtual IProperties * getInput ()
 
virtual IProperties * getOutput ()
 
virtual IProperties * getInfo ()
 
virtual dp::IDispatcher * getDispatcher ()
 
virtual TimeInfo & getTimeInfo ()
 
virtual IProperties * getSystemInfo ()
 
template<typename Item >
dp::Iterator< Item > * createIterator (dp::Iterator< Item > *iter, size_t nbIterations=0, const char *message=0, dp::IteratorListener *listener=0)
 
virtual dp::IteratorListener * createIteratorListener (size_t nbIterations, const char *message)
 
- Public Member Functions inherited from SmartPointer
void use ()
 
void forget ()
 
- Public Member Functions inherited from ISmartPointer
virtual ~ISmartPointer ()
 

Static Public Member Functions

static tools::misc::IOptionsParser * getOptionsParser ()
 
- Static Public Member Functions inherited from Algorithm
template<template< size_t > class Functor>
static int mainloop (tools::misc::IOptionsParser *parser, int argc, char *argv[])
 

Additional Inherited Members

- Protected Member Functions inherited from Algorithm
std::string getUriByKey (const std::string &key)
 
std::string getUri (const std::string &str)
 
void setInput (IProperties *input)
 
- Protected Member Functions inherited from SmartPointer
 SmartPointer ()
 
virtual ~SmartPointer ()
 

Detailed Description

template<size_t span = KMER_DEFAULT_SPAN>
class gatb::core::debruijn::impl::UnitigsConstructionAlgorithm< span >

Computation of the unitigs of a Graph, using BCALM 2.

Constructor & Destructor Documentation

UnitigsConstructionAlgorithm ( tools::storage::impl::Storage &  storage,
std::string  unitigs_filename,
size_t  nb_cores = 0,
tools::misc::IProperties *  options = 0,
bool  do_bcalm = true,
bool  do_bglue = true,
bool  do_links = true 
)

Constructor.

Parameters
[in]graph: graph from which we look for branching nodes
[in]nb_cores: number of cores to be used; 0 means all available cores
[in]options: extra options
~UnitigsConstructionAlgorithm ( )

Destructor.

Member Function Documentation

void execute ( )
virtual

Execution of the algorithm. Abstract method, must be refined in subclasses.

Implements Algorithm.

static tools::misc::IOptionsParser* getOptionsParser ( )
static

Get an option parser for branching parameters. Dynamic allocation, so must be released when no more used.

Returns
an instance of IOptionsParser.
The documentation for this class was generated from the following files: