gatb.core-API-1.4.2
BankConverterAlgorithm Class Reference

Algorithm implementation that converts a bank into a binary one. More...

#include <BankConverterAlgorithm.hpp>

Inheritance diagram for BankConverterAlgorithm:
Inheritance graph

Public Member Functions

 BankConverterAlgorithm (IBank *bank, size_t kmerSize, const std::string &outputUri)
 
 BankConverterAlgorithm (tools::storage::impl::Storage &storage)
 
 ~BankConverterAlgorithm ()
 
void execute ()
 
IBankgetResult ()
 
- 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 IPropertiesgetInput ()
 
virtual IPropertiesgetOutput ()
 
virtual IPropertiesgetInfo ()
 
virtual dp::IDispatchergetDispatcher ()
 
virtual TimeInfogetTimeInfo ()
 
virtual IPropertiesgetSystemInfo ()
 
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::IteratorListenercreateIteratorListener (size_t nbIterations, const char *message)
 
- Public Member Functions inherited from SmartPointer
void use ()
 
void forget ()
 
- Public Member Functions inherited from ISmartPointer
virtual ~ISmartPointer ()
 

Additional Inherited Members

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

Algorithm implementation that converts a bank into a binary one.

This algorithm converts an input IBank instance into a binary output bank.

It subclasses gatb::core::tools::misc::impl::Algorithm in order to get all the features of its parent class.

Historically, it was used by DSK to work on a binary bank instead of a FASTA bank (ie. less I/O operations because of smaller size of binary banks)

Constructor & Destructor Documentation

BankConverterAlgorithm ( IBank bank,
size_t  kmerSize,
const std::string &  outputUri 
)

Constructor.

Parameters
[in]bank: bank to be converted (likely in FASTA format)
[in]kmerSize: kmer size
[in]outputUri: uri of the output binary bank.

Constructor. Used only to retrieved statistics/information gathered during a previous execution of a BankConverterAlgorithm instance

Parameters
[in]storage: storage instance where we get information from.

Destructor.

Member Function Documentation

void execute ( )
virtual

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

Implements Algorithm.

IBank* getResult ( )
inline

Return the output binary bank

Returns
the IBank instance

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