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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)


Detailed Description

Include file for all the AMOS integer types.

Author:
Adam M Phillippy
Date:
11/12/2003

Definition in file inttypes_AMOS.hh.


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  )     swap16(x)
 

big-endian to host 16-bits

Definition at line 216 of file inttypes_AMOS.hh.

#define btoh32  )     swap32(x)
 

big-endian to host 32-bits

Definition at line 217 of file inttypes_AMOS.hh.

#define btoh64  )     swap64(x)
 

big-endian to host 64-bits

Definition at line 218 of file inttypes_AMOS.hh.

#define htob16  )     swap16(x)
 

host to big-endian 16-bits

Definition at line 213 of file inttypes_AMOS.hh.

#define htob32  )     swap32(x)
 

host to big-endian 32-bits

Definition at line 214 of file inttypes_AMOS.hh.

#define htob64  )     swap64(x)
 

host to big-endian 64-bits

Definition at line 215 of file inttypes_AMOS.hh.

#define htol16  )     (x)
 

host to little-endian 16-bits

Definition at line 196 of file inttypes_AMOS.hh.

Referenced by AMOS::writeLE().

#define htol32  )     (x)
 

host to little-endian 32-bits

Definition at line 197 of file inttypes_AMOS.hh.

Referenced by AMOS::writeLE().

#define htol64  )     (x)
 

host to little-endian 64-bits

Definition at line 198 of file inttypes_AMOS.hh.

Referenced by AMOS::writeLE().

#define ltoh16  )     (x)
 

little-endian to host 16-bits

Definition at line 199 of file inttypes_AMOS.hh.

Referenced by AMOS::readLE().

#define ltoh32  )     (x)
 

little-endian to host 32-bits

Definition at line 200 of file inttypes_AMOS.hh.

Referenced by AMOS::readLE().

#define ltoh64  )     (x)
 

little-endian to host 64-bits

Definition at line 201 of file inttypes_AMOS.hh.

Referenced by AMOS::readLE().

#define swap16  )     ((((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  ) 
 

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  ) 
 

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.


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().


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().


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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