inttypes_AMOS.hh File Reference

Include file for all the AMOS integer types. More...

#include <inttypes.h>
#include <limits.h>
#include <string>

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Namespaces
namespace	AMOS
Classes
struct	AMOS::BankFlags_t
	8 bit flag set for IBankable types More...
Defines
#define	__inttypes_AMOS_HH   1
	ints of the form [u]int(size)_t, i.e. int32_t
#define	swap16(x)   ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8))
	swaps the bytes in a 16-bit value
#define	swap32(x)
	swaps the bytes in a 32-bit value
#define	swap64(x)
	swaps the bytes in a 64-bit value
#define	htol16(x)   (x)
	host to little-endian 16-bits
#define	htol32(x)   (x)
	host to little-endian 32-bits
#define	htol64(x)   (x)
	host to little-endian 64-bits
#define	ltoh16(x)   (x)
	little-endian to host 16-bits
#define	ltoh32(x)   (x)
	little-endian to host 32-bits
#define	ltoh64(x)   (x)
	little-endian to host 64-bits
#define	htob16(x)   swap16(x)
	host to big-endian 16-bits
#define	htob32(x)   swap32(x)
	host to big-endian 32-bits
#define	htob64(x)   swap64(x)
	host to big-endian 64-bits
#define	btoh16(x)   swap16(x)
	big-endian to host 16-bits
#define	btoh32(x)   swap32(x)
	big-endian to host 32-bits
#define	btoh64(x)   swap64(x)
	big-endian to host 64-bits
Typedefs
typedef uint32_t	ID_t
	ID type for iid's.
typedef uint32_t	NCode_t
	unique integer code for dynamic typing
typedef uint32_t	SD_t
	standard deviation type
typedef int32_t	Size_t
	size type (for links,etc)
typedef Size_t	Pos_t
	position type (in a sequence,etc)
typedef char	Status_t
	status type
Functions
char	Qual2Char (uint8_t qual)
	Converts a quality int into a printable character.
uint8_t	Char2Qual (char qual)
	Converts a printable quality character to an int.
std::string	Decode (NCode_t ncode)
	Converts an NCode integer to an AMOS message/field type.
NCode_t	Encode (const std::string &str)
	Converts an AMOS message/field type to an NCode integer.
Variables
const uint8_t	NCODE_SIZE = 3
	length of the NCode strings
const NCode_t	NULL_NCODE = 0
	NULL NCode definition.
const ID_t	NULL_ID = 0
	NULL ID definition.
const Status_t	NULL_STATUS = 0
	NULL status definition.
const char	MIN_QUALITY = '0'
	min quality score definition
const char	MAX_QUALITY = '0' + 63
	max quality score definition
const char	NULL_CHAR = '\0'
	null char
const char	NL_CHAR = '\n'
	newline char
const std::string	NULL_STRING = &NULL_CHAR
	null string
const ID_t	MAX_ID = ~((uint32_t)0)
	(unsigned 32bit int)
const Size_t	MAX_SIZE = ~((uint32_t)0) >> 1
	( signed 32bit int)
const Pos_t	MAX_POS = ~((uint32_t)0) >> 1
	( signed 32bit int)

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Detailed Description

Include file for all the AMOS integer types.

Author:

Adam M Phillippy

Date:

11/12/2003

Definition in file inttypes_AMOS.hh.

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Define Documentation

#define __inttypes_AMOS_HH   1

ints of the form [u]int(size)_t, i.e. int32_t Definition at line 11 of file inttypes_AMOS.hh.

#define btoh16 (  x   )     swap16(x)

big-endian to host 16-bits Definition at line 216 of file inttypes_AMOS.hh.

#define btoh32 (  x   )     swap32(x)

big-endian to host 32-bits Definition at line 217 of file inttypes_AMOS.hh.

#define btoh64 (  x   )     swap64(x)

big-endian to host 64-bits Definition at line 218 of file inttypes_AMOS.hh.

#define htob16 (  x   )     swap16(x)

host to big-endian 16-bits Definition at line 213 of file inttypes_AMOS.hh.

#define htob32 (  x   )     swap32(x)

host to big-endian 32-bits Definition at line 214 of file inttypes_AMOS.hh.

#define htob64 (  x   )     swap64(x)

host to big-endian 64-bits Definition at line 215 of file inttypes_AMOS.hh.

#define htol16 (  x   )     (x)

host to little-endian 16-bits Definition at line 196 of file inttypes_AMOS.hh. Referenced by AMOS::writeLE().

#define htol32 (  x   )     (x)

host to little-endian 32-bits Definition at line 197 of file inttypes_AMOS.hh. Referenced by AMOS::writeLE().

#define htol64 (  x   )     (x)

host to little-endian 64-bits Definition at line 198 of file inttypes_AMOS.hh. Referenced by AMOS::writeLE().

#define ltoh16 (  x   )     (x)

little-endian to host 16-bits Definition at line 199 of file inttypes_AMOS.hh. Referenced by AMOS::readLE().

#define ltoh32 (  x   )     (x)

little-endian to host 32-bits Definition at line 200 of file inttypes_AMOS.hh. Referenced by AMOS::readLE().

#define ltoh64 (  x   )     (x)

little-endian to host 64-bits Definition at line 201 of file inttypes_AMOS.hh. Referenced by AMOS::readLE().

#define swap16 (  x   )     ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8))

swaps the bytes in a 16-bit value Definition at line 152 of file inttypes_AMOS.hh.

#define swap32 (  x   )

Value: ((((x) & 0xff000000) >> 24) | (((x) & 0x00ff0000) >> 8) \ | (((x) & 0x0000ff00) << 8) | (((x) & 0x000000ff) << 24)) swaps the bytes in a 32-bit value Definition at line 158 of file inttypes_AMOS.hh.

#define swap64 (  x   )

Value: ((((x) & 0xff00000000000000ull) >> 56) \ | (((x) & 0x00ff000000000000ull) >> 40) \ | (((x) & 0x0000ff0000000000ull) >> 24) \ | (((x) & 0x000000ff00000000ull) >> 8) \ | (((x) & 0x00000000ff000000ull) << 8) \ | (((x) & 0x0000000000ff0000ull) << 24) \ | (((x) & 0x000000000000ff00ull) << 40) \ | (((x) & 0x00000000000000ffull) << 56)) swaps the bytes in a 64-bit value Definition at line 166 of file inttypes_AMOS.hh.

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Typedef Documentation

typedef uint32_t AMOS::ID_t

ID type for iid's. Definition at line 24 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::assignEID(), AMOS::Bank_t::assignIID(), AMOS::Bank_t::concat(), AMOS::Index_t::count(), AMOS::IDMap_t::exists(), AMOS::BankStream_t::existsIID(), AMOS::Bank_t::existsIID(), AMOS::Bank_t::fetch(), AMOS::Bank_t::fetchBID(), AMOS::Read_t::getFragment(), AMOS::IBankable_t::getIID(), AMOS::Fragment_t::getLibrary(), AMOS::BankStream_t::getMaxIID(), AMOS::Bank_t::getMaxIID(), AMOS::Link_t::getNodes(), AMOS::Bank_t::getPartition(), AMOS::IDMap_t::HashTriple_t::HashTriple_t(), AMOS::BankStream_t::ignore(), AMOS::Index_t::insert(), AMOS::IDMap_t::insert(), AMOS::Index_t::isMulti(), AMOS::Bank_t::localizeBID(), AMOS::Index_t::lookup(), AMOS::Index_t::lookupAll(), AMOS::IDMap_t::lookupBID(), AMOS::BankStream_t::lookupBID(), AMOS::Bank_t::lookupBID(), AMOS::IDMap_t::lookupEID(), AMOS::BankStream_t::lookupEID(), AMOS::Bank_t::lookupEID(), AMOS::IDMap_t::lookupIID(), AMOS::BankStream_t::lookupIID(), AMOS::Bank_t::lookupIID(), main(), AMOS::Bank_t::openPartition(), AMOS::BankStream_t::operator>>(), AMOS::IDMap_t::read(), AMOS::Scaffold_t::readMessage(), AMOS::Kmer_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::IEdge_t::readMessage(), AMOS::Index_t::remove(), AMOS::IDMap_t::remove(), AMOS::Bank_t::remove(), AMOS::Bank_t::removeBID(), AMOS::Bank_t::replace(), AMOS::Bank_t::replaceBID(), AMOS::BankStream_t::seekg(), AMOS::Read_t::setFragment(), AMOS::IBankable_t::setIID(), AMOS::Fragment_t::setLibrary(), AMOS::IEdge_t::setLinks(), AMOS::Bank_t::syncIFO(), AMOS::BankStream_t::tellg(), and AMOS::BankStream_t::tellp().

typedef uint32_t AMOS::NCode_t

unique integer code for dynamic typing Definition at line 25 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::Bank_t(), AMOS::BankExists(), AMOS::BankStream_t::BankStream_t(), AMOS::Decode(), AMOS::Encode(), AMOS::BankStreamSet_t::exists(), AMOS::BankSet_t::exists(), AMOS::UniversalSet_t::exists(), AMOS::Message_t::exists(), AMOS::Message_t::getField(), AMOS::Group_t::getMemberType(), AMOS::Message_t::getMessageCode(), AMOS::Universal_t::getNCode(), AMOS::Sequence_t::getNCode(), AMOS::ScaffoldLink_t::getNCode(), AMOS::ScaffoldEdge_t::getNCode(), AMOS::Scaffold_t::getNCode(), AMOS::Read_t::getNCode(), AMOS::Overlap_t::getNCode(), AMOS::Link_t::getNCode(), AMOS::Library_t::getNCode(), AMOS::Layout_t::getNCode(), AMOS::Kmer_t::getNCode(), AMOS::Index_t::getNCode(), AMOS::IDMap_t::getNCode(), AMOS::Group_t::getNCode(), AMOS::Fragment_t::getNCode(), AMOS::Feature_t::getNCode(), AMOS::Edge_t::getNCode(), AMOS::Tile_t::getNCode(), AMOS::Distribution_t::getNCode(), AMOS::ContigLink_t::getNCode(), AMOS::ContigEdge_t::getNCode(), AMOS::Contig_t::getNCode(), AMOS::ScaffoldLink_t::getNodeType(), AMOS::Link_t::getNodeType(), AMOS::ContigLink_t::getNodeType(), AMOS::IDMap_t::getType(), AMOS::BankStream_t::getType(), AMOS::Bank_t::getType(), AMOS::Index_t::Index_t(), AMOS::BankStreamSet_t::operator[](), AMOS::BankSet_t::operator[](), AMOS::UniversalSet_t::operator[](), AMOS::Message_t::operator[](), AMOS::Message_t::removeField(), AMOS::IDMap_t::resize(), AMOS::Message_t::setField(), AMOS::Group_t::setMemberType(), AMOS::Message_t::setMessageCode(), AMOS::Link_t::setNodeType(), AMOS::Index_t::setType(), AMOS::IDMap_t::setType(), AMOS::Message_t::skip(), and AMOS::Bank_t::syncIFO().

typedef Size_t AMOS::Pos_t

position type (in a sequence,etc) Definition at line 28 of file inttypes_AMOS.hh. Referenced by AMOS::Sequence_t::compress(), AMOS::Contig_t::gap2ungap(), AMOS::Sequence_t::getBase(), AMOS::Kmer_t::getBase(), AMOS::Range_t::getBegin(), AMOS::Range_t::getEnd(), AMOS::Read_t::getFragmentPosition(), AMOS::Range_t::getHi(), AMOS::Range_t::getLo(), AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), AMOS::Kmer_t::getSeqString(), AMOS::Scaffold_t::getSpan(), AMOS::Layout_t::getSpan(), AMOS::Contig_t::getSpan(), AMOS::Contig_t::getUngappedLength(), AMOS::Contig_t::getUngappedQualString(), AMOS::Contig_t::getUngappedSeqString(), AMOS::operator &(), AMOS::operator|(), AMOS::Range_t::Range_t(), AMOS::Tile_t::readMessage(), AMOS::Scaffold_t::readRecord(), AMOS::Read_t::readRecord(), AMOS::Layout_t::readRecord(), AMOS::Kmer_t::readRecord(), AMOS::Index_t::readRecord(), AMOS::Group_t::readRecord(), AMOS::IEdge_t::readRecord(), AMOS::Tile_t::readRecord(), AMOS::Contig_t::readRecord(), AMOS::Sequence_t::setBase(), AMOS::Kmer_t::setBase(), AMOS::Range_t::setBegin(), AMOS::Range_t::setEnd(), AMOS::Read_t::setFragmentPosition(), AMOS::Range_t::setRange(), AMOS::Kmer_t::setSeqString(), AMOS::Sequence_t::setSequence(), AMOS::Range_t::swap(), AMOS::Sequence_t::uncompress(), AMOS::Contig_t::ungap2gap(), AMOS::Sequence_t::writeMessage(), AMOS::Scaffold_t::writeMessage(), AMOS::Layout_t::writeMessage(), AMOS::Contig_t::writeMessage(), AMOS::Scaffold_t::writeRecord(), AMOS::Read_t::writeRecord(), AMOS::Layout_t::writeRecord(), AMOS::Kmer_t::writeRecord(), AMOS::Group_t::writeRecord(), AMOS::IEdge_t::writeRecord(), AMOS::Tile_t::writeRecord(), and AMOS::Contig_t::writeRecord().

typedef uint32_t AMOS::SD_t

standard deviation type Definition at line 26 of file inttypes_AMOS.hh. Referenced by AMOS::Link_t::getSD(), and AMOS::Link_t::setSD().

typedef int32_t AMOS::Size_t

size type (for links,etc) Definition at line 27 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::appendBID(), AMOS::Bank_t::BankPartition_t::BankPartition_t(), AMOS::Bank_t::clean(), AMOS::Bank_t::clear(), AMOS::Bank_t::close(), AMOS::Bank_t::concat(), AMOS::Index_t::count(), AMOS::Message_t::countFields(), AMOS::Message_t::countSubMessages(), AMOS::Overlap_t::flip(), AMOS::Overlap_t::getAhang(), AMOS::Overlap_t::getBhang(), AMOS::IDMap_t::getBuckets(), AMOS::Tile_t::getGappedLength(), AMOS::BankStream_t::getIDMapSize(), AMOS::Bank_t::getIDMapSize(), AMOS::Bank_t::getIndexSize(), AMOS::Sequence_t::getLength(), AMOS::Range_t::getLength(), AMOS::BankStreamSet_t::getSize(), AMOS::BankSet_t::getSize(), AMOS::UniversalSet_t::getSize(), AMOS::Link_t::getSize(), AMOS::Index_t::getSize(), AMOS::IDMap_t::getSize(), AMOS::Fragment_t::getSize(), AMOS::BankStream_t::getSize(), AMOS::Bank_t::getSize(), AMOS::Scaffold_t::getSpan(), AMOS::Layout_t::getSpan(), AMOS::Contig_t::getSpan(), AMOS::Contig_t::getUngappedLength(), AMOS::IDMap_t::IDMap_t(), AMOS::BankStream_t::ignore(), AMOS::Bank_t::openPartition(), AMOS::BankStream_t::operator<<(), AMOS::Kmer_t::operator=(), AMOS::BankStream_t::operator>>(), AMOS::IDMap_t::read(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Scaffold_t::readRecord(), AMOS::Read_t::readRecord(), AMOS::Layout_t::readRecord(), AMOS::Kmer_t::readRecord(), AMOS::Index_t::readRecord(), AMOS::Group_t::readRecord(), AMOS::IEdge_t::readRecord(), AMOS::Tile_t::readRecord(), AMOS::Contig_t::readRecord(), AMOS::Index_t::remove(), AMOS::Bank_t::replaceBID(), AMOS::IDMap_t::resize(), AMOS::Overlap_t::setAhang(), AMOS::Overlap_t::setBhang(), AMOS::Kmer_t::setSeqString(), AMOS::Sequence_t::setSequence(), AMOS::Link_t::setSize(), AMOS::Fragment_t::setSize(), AMOS::Bank_t::syncIFO(), AMOS::Contig_t::ungap2gap(), AMOS::Sequence_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::Scaffold_t::writeRecord(), AMOS::Read_t::writeRecord(), AMOS::Layout_t::writeRecord(), AMOS::Kmer_t::writeRecord(), AMOS::Index_t::writeRecord(), AMOS::Group_t::writeRecord(), AMOS::IEdge_t::writeRecord(), AMOS::Tile_t::writeRecord(), and AMOS::Contig_t::writeRecord().

typedef char AMOS::Status_t

status type Definition at line 29 of file inttypes_AMOS.hh. Referenced by AMOS::Universal_t::getStatus(), and AMOS::Universal_t::setStatus().

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Function Documentation

uint8_t Char2Qual (  char  qual  )  [inline]

Converts a printable quality character to an int. Parameters: qual  Character quality representation Returns: Integer quality representation Definition at line 64 of file inttypes_AMOS.hh. References AMOS::MIN_QUALITY. Referenced by AMOS::Sequence_t::compress().

std::string Decode (  NCode_t  ncode  )  [inline]

Converts an NCode integer to an AMOS message/field type. Parameters: ncode  The NCode to translate to a string Returns: String representation of the NCode Definition at line 76 of file inttypes_AMOS.hh. References AMOS::NCode_t. Referenced by AMOS::BankExists(), AMOS::Bank_t::create(), AMOS::Bank_t::exists(), AMOS::Message_t::getField(), main(), AMOS::Bank_t::open(), AMOS::BankStreamSet_t::operator[](), AMOS::BankSet_t::operator[](), AMOS::UniversalSet_t::operator[](), AMOS::Message_t::read(), AMOS::Bank_t::syncIFO(), AMOS::Message_t::write(), AMOS::IDMap_t::write(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), AMOS::Group_t::writeMessage(), AMOS::Fragment_t::writeMessage(), and AMOS::Feature_t::writeMessage().

NCode_t Encode (  const std::string &  str  )  [inline]

Converts an AMOS message/field type to an NCode integer. Parameters: str  The NCode string equivalent Precondition: str is of proper NCode length, i.e. str . size( ) == NCODE_SIZE Returns: NCode of the string Definition at line 91 of file inttypes_AMOS.hh. References AMOS::NCode_t. Referenced by AMOS::Bank_t::Bank_t(), AMOS::Message_t::exists(), AMOS::Message_t::getField(), AMOS::BankStreamSet_t::operator[](), AMOS::BankSet_t::operator[](), AMOS::UniversalSet_t::operator[](), AMOS::IDMap_t::read(), AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Message_t::removeField(), AMOS::Message_t::setField(), AMOS::Message_t::setMessageCode(), and AMOS::Message_t::skip().

char Qual2Char (  uint8_t  qual  )  [inline]

Converts a quality int into a printable character. Parameters: qual  Integer quality representation Returns: Printable quality character Definition at line 52 of file inttypes_AMOS.hh. References AMOS::MIN_QUALITY. Referenced by AMOS::Sequence_t::uncompress().

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Variable Documentation

const ID_t AMOS::MAX_ID = ~((uint32_t)0)

(unsigned 32bit int) Definition at line 41 of file inttypes_AMOS.hh.

const Pos_t AMOS::MAX_POS = ~((uint32_t)0) >> 1

( signed 32bit int) Definition at line 43 of file inttypes_AMOS.hh. Referenced by AMOS::Scaffold_t::getSpan(), and AMOS::Layout_t::getSpan().

const char AMOS::MAX_QUALITY = '0' + 63

max quality score definition Definition at line 36 of file inttypes_AMOS.hh.

const Size_t AMOS::MAX_SIZE = ~((uint32_t)0) >> 1

( signed 32bit int) Definition at line 42 of file inttypes_AMOS.hh.

const char AMOS::MIN_QUALITY = '0'

min quality score definition Definition at line 35 of file inttypes_AMOS.hh. Referenced by AMOS::Char2Qual(), and AMOS::Qual2Char().

const uint8_t AMOS::NCODE_SIZE = 3

length of the NCode strings Definition at line 31 of file inttypes_AMOS.hh. Referenced by AMOS::Message_t::read(), AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), and AMOS::Message_t::skip().

const char AMOS::NL_CHAR = '\n'

newline char Definition at line 38 of file inttypes_AMOS.hh. Referenced by AMOS::Message_t::read(), AMOS::IBankable_t::setEID(), AMOS::Message_t::setField(), AMOS::Kmer_t::setSeqString(), AMOS::Sequence_t::setSequence(), AMOS::Message_t::skip(), AMOS::Message_t::write(), AMOS::IDMap_t::write(), AMOS::Sequence_t::writeMessage(), AMOS::Index_t::writeMessage(), and AMOS::IDMap_t::writeMessage().

const char AMOS::NULL_CHAR = '\0'

null char Definition at line 37 of file inttypes_AMOS.hh. Referenced by AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), AMOS::Kmer_t::getSeqString(), AMOS::Message_t::read(), AMOS::Message_t::skip(), and AMOS::Bank_t::syncIFO().

const ID_t AMOS::NULL_ID = 0

NULL ID definition. Definition at line 33 of file inttypes_AMOS.hh. Referenced by AMOS::BankStream_t::BankStream_t(), AMOS::Index_t::buildContigFeature(), AMOS::Index_t::buildContigScaffold(), AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildReadMate(), AMOS::Index_t::buildScaffoldFeature(), AMOS::Read_t::clear(), AMOS::Overlap_t::clear(), AMOS::Link_t::clear(), AMOS::Fragment_t::clear(), AMOS::Feature_t::clear(), AMOS::Tile_t::clear(), AMOS::IBankable_t::clear(), AMOS::Bank_t::clear(), AMOS::Feature_t::Feature_t(), AMOS::Fragment_t::Fragment_t(), AMOS::Bank_t::getMaxIID(), AMOS::IBankable_t::IBankable_t(), AMOS::Bank_t::init(), AMOS::IDMap_t::insert(), AMOS::Link_t::Link_t(), AMOS::IDMap_t::lookupBID(), AMOS::Bank_t::lookupBID(), AMOS::IDMap_t::lookupIID(), AMOS::BankStream_t::operator>>(), AMOS::Overlap_t::Overlap_t(), AMOS::Read_t::Read_t(), AMOS::Kmer_t::readRecord(), AMOS::Group_t::readRecord(), AMOS::IEdge_t::readRecord(), AMOS::IDMap_t::remove(), AMOS::Tile_t::Tile_t(), AMOS::Universal_t::writeMessage(), AMOS::Read_t::writeMessage(), AMOS::Overlap_t::writeMessage(), AMOS::Link_t::writeMessage(), AMOS::Fragment_t::writeMessage(), AMOS::Feature_t::writeMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::NULL_NCODE = 0

NULL NCode definition. Definition at line 32 of file inttypes_AMOS.hh. Referenced by AMOS::Link_t::clear(), AMOS::Index_t::clear(), AMOS::IDMap_t::clear(), AMOS::Group_t::clear(), AMOS::Fragment_t::clear(), AMOS::Feature_t::clear(), AMOS::Feature_t::Feature_t(), AMOS::Fragment_t::Fragment_t(), AMOS::Group_t::Group_t(), AMOS::IDMap_t::IDMap_t(), AMOS::Index_t::Index_t(), AMOS::Link_t::Link_t(), AMOS::Message_t::read(), AMOS::ScaffoldLink_t::readMessage(), AMOS::ContigLink_t::readMessage(), AMOS::ScaffoldLink_t::readRecord(), AMOS::ContigLink_t::readRecord(), AMOS::Message_t::skip(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), AMOS::Group_t::writeMessage(), AMOS::Fragment_t::writeMessage(), and AMOS::Feature_t::writeMessage().

const Status_t AMOS::NULL_STATUS = 0

NULL status definition. Definition at line 34 of file inttypes_AMOS.hh. Referenced by AMOS::Universal_t::clear(), AMOS::Universal_t::Universal_t(), and AMOS::Universal_t::writeMessage().

const std::string AMOS::NULL_STRING = &NULL_CHAR

null string Definition at line 39 of file inttypes_AMOS.hh. Referenced by AMOS::Bank_t::addPartition(), AMOS::IDMap_t::insert(), AMOS::IDMap_t::lookupEID(), main(), AMOS::Universal_t::writeMessage(), AMOS::Scaffold_t::writeMessage(), AMOS::Read_t::writeMessage(), AMOS::Overlap_t::writeMessage(), AMOS::Link_t::writeMessage(), AMOS::Kmer_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), AMOS::Group_t::writeMessage(), AMOS::Fragment_t::writeMessage(), AMOS::Feature_t::writeMessage(), AMOS::IEdge_t::writeMessage(), AMOS::Tile_t::writeMessage(), and AMOS::Distribution_t::writeMessage().

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