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gatb.core-API-0.0.0
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gatb.core-API-0.0.0
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Algorithm implementation that converts a bank into a binary one. More...
#include <BankConverterAlgorithm.hpp>
Public Member Functions | |
| BankConverterAlgorithm (IBank *bank, size_t kmerSize, const std::string &outputUri) | |
| BankConverterAlgorithm (tools::storage::impl::Storage &storage) | |
| ~BankConverterAlgorithm () | |
| void | execute () |
| IBank * | getResult () |
 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 () |
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 () |
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)
| BankConverterAlgorithm | ( | IBank * | bank, |
| size_t | kmerSize, | ||
| const std::string & | outputUri | ||
| ) |
Constructor.
| [in] | bank | : bank to be converted (likely in FASTA format) |
| [in] | kmerSize | : kmer size |
| [in] | outputUri | : uri of the output binary bank. |
| BankConverterAlgorithm | ( | tools::storage::impl::Storage & | storage | ) |
Constructor. Used only to retrieved statistics/information gathered during a previous execution of a BankConverterAlgorithm instance
| [in] | storage | : storage instance where we get information from. |
Destructor.
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virtual |
Execution of the algorithm. Abstract method, must be refined in subclasses.
Implements Algorithm.
1.8.11 
