Bank_AMOS.hh File Reference

Header for Bank_t. More...

#include "utility_AMOS.hh"
#include "IDMap_AMOS.hh"
#include <cstdlib>
#include <string>
#include <fstream>
#include <vector>
#include <deque>

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Namespaces
namespace	AMOS
Classes
class	AMOS::IBankable_t
	Interface for classes that can be stored in an AMOS bank. More...
class	AMOS::Bank_t
	An AMOS data bank for efficiently storing Bankable data types. More...
class	AMOS::Bank_t::BankPartition_t
	A single partition of the file-based bank. More...
Defines
#define	__Bank_AMOS_HH   1
Typedefs
typedef uint8_t	BankMode_t
Functions
bool	BankExists (NCode_t ncode, const std::string &dir)
	Checks for the accessibility of a bank with certain type.
void	PrintBankVersion (const char *s)
	Prints the bank version a program is compatible with.
Variables
const BankMode_t	B_READ = 0x1
	protected reading mode
const BankMode_t	B_WRITE = 0x2
	protected writing mode
const BankMode_t	B_SPY = 0x4
	unprotected reading mode, overrides all other modes

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Detailed Description

Header for Bank_t.

Author:

Adam M Phillippy

Date:

07/18/2003

Definition in file Bank_AMOS.hh.

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Define Documentation

#define __Bank_AMOS_HH   1

Note: In an effort to ensure the binary-compatibility of AMOS banks all disk I/O should be independent of any system-dependent sizes or byte orders (endian-ness), such as 'int' which can vary in size and be stored in either big- or little-endian byte order. To avoid these issues, use only types with known sizes (int32_t for example) and read/write atomic data with the readLE and writeLE methods which convert strongly-typed ints to and from little-endian byte order before reading/writing. Definition at line 20 of file Bank_AMOS.hh.

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Typedef Documentation

typedef uint8_t AMOS::BankMode_t

Definition at line 34 of file Bank_AMOS.hh. Referenced by AMOS::BankStream_t::create(), AMOS::Bank_t::create(), AMOS::BankStream_t::open(), AMOS::Bank_t::open(), and AMOS::Bank_t::setMode().

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Function Documentation

bool AMOS::BankExists (  NCode_t  ncode, const std::string &  dir )

Checks for the accessibility of a bank with certain type. Only checks for the existence and readability of the info store, does not perform any validity checking on the other partitions. Parameters: ncode  The type of bank to look for dir  The directory in which to look Returns: true if IFO store exists with read permissions, else false Definition at line 1030 of file Bank_AMOS.cc. References AMOS::Decode(), and AMOS::NCode_t.

void AMOS::PrintBankVersion (  const char *  s  )

Prints the bank version a program is compatible with. Parameters: s  The program name Returns: void Definition at line 1041 of file Bank_AMOS.cc.

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Variable Documentation

const BankMode_t AMOS::B_READ = 0x1

protected reading mode Definition at line 35 of file Bank_AMOS.hh. Referenced by AMOS::Index_t::buildContigFeature(), AMOS::Index_t::buildContigScaffold(), AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildScaffoldFeature(), AMOS::Bank_t::clean(), AMOS::Bank_t::concat(), AMOS::Bank_t::fetchBID(), AMOS::BankStream_t::ignore(), AMOS::BankStream_t::operator>>(), AMOS::Bank_t::removeBID(), AMOS::Bank_t::replaceBID(), AMOS::BankStream_t::seekg(), AMOS::Bank_t::setMode(), and AMOS::Bank_t::syncIFO().

const BankMode_t AMOS::B_SPY = 0x4

unprotected reading mode, overrides all other modes Definition at line 37 of file Bank_AMOS.hh. Referenced by AMOS::Bank_t::lockIFO(), AMOS::Bank_t::setMode(), AMOS::Bank_t::syncIFO(), AMOS::Bank_t::touchFile(), and AMOS::Bank_t::unlockIFO().

const BankMode_t AMOS::B_WRITE = 0x2

protected writing mode Definition at line 36 of file Bank_AMOS.hh. Referenced by AMOS::Bank_t::appendBID(), AMOS::Bank_t::clean(), AMOS::Bank_t::clear(), AMOS::Bank_t::close(), AMOS::Bank_t::concat(), AMOS::Bank_t::create(), AMOS::Bank_t::destroy(), AMOS::Bank_t::openPartition(), AMOS::BankStream_t::operator<<(), AMOS::Bank_t::removeBID(), AMOS::Bank_t::replaceBID(), AMOS::Bank_t::setMode(), and AMOS::Bank_t::syncIFO().

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