libAMOS: AMOS Namespace Reference


Classes
class	IBankable_t
	Interface for classes that can be stored in an AMOS bank. More...
class	Bank_t
	An AMOS data bank for efficiently storing Bankable data types. More...
class	BankStream_t
	Provides stream functionality for an AMOS data bank. More...
class	Contig_t
	A tiling of assembled sequence reads. More...
class	ContigEdge_t
	Reliable linking information between two contigs. More...
class	TiledRead_t
	A read within a contig "rendered" with gaps inserted. More...
struct	TileOrderCmp
	A binary function for determining the canonical sort order for reads. More...
class	BaseStats_t
	Maintains statistics the Column_t about reads which share the same base at the current position. More...
struct	BaseStatsCmp
	Functor for sorting BaseStats_t by count of reads of each base, then cumqv, then maxqv. More...
class	Column_t
	Maintains data on reads at a given contig position. More...
class	ContigIterator_t
	Used for iterating through a contig on a per-consensus position basis. More...
class	ContigLink_t
	Linking information between two contigs. More...
struct	Distribution_t
	A set of statistics that define a distribution. More...
struct	Range_t
	A gapped coordinate range. More...
struct	Tile_t
	A singe sequence's location and orientation in a larger sequence. More...
class	IEdge_t
	Interface for Edge_t. More...
class	Edge_t
	Reliable linking information between two nodes. More...
class	Exception_t
	The base AMOS excpetion class. More...
class	AlignmentException_t
	An exception for alignment failures. More...
class	AllocException_t
	An exception for alloc failures, better than std::bad_alloc. More...
class	ArgumentException_t
	An exception for invalid arguments. More...
class	IOException_t
	An exception for IO errors. More...
class	Feature_t
	Notes remarkable features of other objects. More...
class	Fragment_t
	Single piece of DNA. More...
class	Group_t
	A homogenous grouping of AMOS objects. More...
class	IDMap_t
	An IID/EID double hash for mapping IIDs and EIDs to BIDs. More...
class	Index_t
	An association index between two types of AMOS objects. More...
struct	BankFlags_t
	8 bit flag set for IBankable types More...
class	Kmer_t
	String of K bases present in the assembly. More...
class	Layout_t
	A layout of sequences. More...
class	Library_t
	A collection of cloned, size-controlled DNA molecules. More...
class	Link_t
	Linking information between two nodes, such as between contigs. More...
class	Message_t
	A generic AMOS message object for reading and writing data. More...
class	IMessagable_t
	Interface for classes that can interpret messages. More...
class	Overlap_t
	An overlap relation between to sequencing reads. More...
class	Read_t
	A DNA sequencing read. More...
class	Scaffold_t
	A ordered, oriented and positioned list of contigs. More...
class	ScaffoldEdge_t
	Reliable linking information between two scaffolds. More...
class	ScaffoldLink_t
	Linking information between two scaffolds. More...
class	Sequence_t
	Sequence bases with quality scores. More...
class	Universal_t
	A universal base class that can be used by Banks or Messages. More...
class	UniversalSet_t
	A non-redundant, complete collection of Universal objects. More...
class	BankSet_t
	A non-redundant, complete collection of AMOS banks. More...
class	BankStreamSet_t
	A non-redundant, complete collection of AMOS banks. More...
Typedefs
typedef uint8_t	BankMode_t
typedef std::list< TiledRead_t >	TiledReadList_t
typedef Range_t	Ordered_Range_t
typedef char	FeatureType_t
typedef char	FragmentType_t
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
typedef char	LinkType_t
typedef char	LinkAdjacency_t
typedef char	OverlapAdjacency_t
typedef char	ReadType_t
Functions
bool	BankExists (NCode_t ncode, const string &dir)
void	PrintBankVersion (const char *s)
	Prints the bank version a program is compatible with.
bool	BankExists (NCode_t ncode, const std::string &dir)
	Checks for the accessibility of a bank with certain type.
Range_t	operator & (Range_t a, Range_t b)
	An intersection operator for Ranges.
Range_t	operator\| (Range_t a, Range_t b)
	A union operator for Ranges.
bool	operator== (const Range_t &a, const Range_t &b)
	An equality operator for Ranges.
bool	operator!= (const Range_t &a, const Range_t &b)
bool	operator== (const Distribution_t &a, const Distribution_t &b)
	An equality operator for Distributions.
bool	operator!= (const Distribution_t &a, const Distribution_t &b)
bool	operator== (const Tile_t &a, const Tile_t &b)
	An equality operator for Tiles.
bool	operator!= (const Tile_t &a, const Tile_t &b)
void	WrapString (ostream &out, const string &s, int per)
void	WrapString (std::ostream &out, const std::string &s, int per)
	Inserts a newline every 'per' characters when writing to stream.
std::ostream &	operator<< (std::ostream &out, const Exception_t &e)
	Dump Exception_t info to an ostream.
std::ostream &	operator<< (std::ostream &out, const std::exception &e)
	Dump exception info to an ostream.
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.
ostream &	operator<< (ostream &out, Read_t &read)
std::ostream &	operator<< (std::ostream &o, Read_t &read)
	Dump read object to ostream.
char	Complement (char ch)
	Returns the DNA complement of an IUPAC character.
void	ReverseComplement (string &str)
void	ReverseComplement (char *str)
	Takes the DNA reverse complement of an IUPAC string.
void	Reverse (string &str)
void	Reverse (char *str)
	Reverses the contents of a string.
void *	SafeCalloc (size_t num, size_t size)
	Safe calloc wrapper.
void *	SafeMalloc (size_t size)
	Safe malloc wrapper.
void *	SafeRealloc (void *P, size_t size)
	Safe realloc wrapper.
char *	SafeStrdup (const char *str)
	Safe strdup wrapper.
void	ReverseComplement (std::string &str)
	Takes the DNA reverse complement of an IUPAC string.
void	Reverse (std::string &str)
	Reverses the contents of a string.
void	writeLE (std::ostream &out, const uint8_t *i)
	Writes an 8-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int8_t *i)
void	writeLE (std::ostream &out, const BankFlags_t *i)
void	writeLE (std::ostream &out, const uint16_t *i)
	Writes a 16-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int16_t *i)
void	writeLE (std::ostream &out, const uint32_t *i)
	Writes a 32-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int32_t *i)
void	writeLE (std::ostream &out, const uint64_t *i)
	Writes a 64-bit int in little-endian byte order.
void	writeLE (std::ostream &out, const int64_t *i)
void	readLE (std::istream &in, uint8_t *i)
	Reads a little-endian 8-bit int.
void	readLE (std::istream &in, int8_t *i)
void	readLE (std::istream &in, BankFlags_t *i)
void	readLE (std::istream &in, uint16_t *i)
	Reads a little-endian 16-bit int.
void	readLE (std::istream &in, int16_t *i)
void	readLE (std::istream &in, uint32_t *i)
	Reads a little-endian 32-bit int.
void	readLE (std::istream &in, int32_t *i)
void	readLE (std::istream &in, uint64_t *i)
	Reads a little-endian 64-bit int.
void	readLE (std::istream &in, int64_t *i)
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
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)
const char	E_ADD = 'A'
const char	E_DELETE = 'D'
const char	E_REPLACE = 'R'
const NCode_t	F_NULL = AMOS_ENCODE ('n','u','l')
const NCode_t	F_AHANG = AMOS_ENCODE ('a','h','g')
const NCode_t	F_ACTION = AMOS_ENCODE ('a','c','t')
const NCode_t	F_ADJACENCY = AMOS_ENCODE ('a','d','j')
const NCode_t	F_BASEPOSITION = AMOS_ENCODE ('b','c','p')
const NCode_t	F_BHANG = AMOS_ENCODE ('b','h','g')
const NCode_t	F_BID = AMOS_ENCODE ('b','i','d')
const NCode_t	F_CLEAR = AMOS_ENCODE ('c','l','r')
const NCode_t	F_COMMENT = AMOS_ENCODE ('c','o','m')
const NCode_t	F_COUNT = AMOS_ENCODE ('c','n','t')
const NCode_t	F_EID = AMOS_ENCODE ('e','i','d')
const NCode_t	F_EDGE = AMOS_ENCODE ('e','d','g')
const NCode_t	F_FLAG = AMOS_ENCODE ('f','l','g')
const NCode_t	F_FRAGMENT = AMOS_ENCODE ('f','r','g')
const NCode_t	F_GAPS = AMOS_ENCODE ('g','a','p')
const NCode_t	F_IID = AMOS_ENCODE ('i','i','d')
const NCode_t	F_LIBRARY = AMOS_ENCODE ('l','i','b')
const NCode_t	F_LINK = AMOS_ENCODE ('l','n','k')
const NCode_t	F_MAP = AMOS_ENCODE ('m','a','p')
const NCode_t	F_MEAN = AMOS_ENCODE ('m','e','a')
const NCode_t	F_MEMBER = AMOS_ENCODE ('m','b','r')
const NCode_t	F_NODES = AMOS_ENCODE ('n','d','s')
const NCode_t	F_OBJECT = AMOS_ENCODE ('o','b','j')
const NCode_t	F_OFFSET = AMOS_ENCODE ('o','f','f')
const NCode_t	F_POSITION = AMOS_ENCODE ('p','o','s')
const NCode_t	F_QUALITY = AMOS_ENCODE ('q','l','t')
const NCode_t	F_QUALITYCLEAR = AMOS_ENCODE ('q','c','r')
const NCode_t	F_READS = AMOS_ENCODE ('r','d','s')
const NCode_t	F_SCORE = AMOS_ENCODE ('s','c','r')
const NCode_t	F_SEQUENCE = AMOS_ENCODE ('s','e','q')
const NCode_t	F_SD = AMOS_ENCODE ('s','t','d')
const NCode_t	F_SIZE = AMOS_ENCODE ('s','z','e')
const NCode_t	F_SOURCE = AMOS_ENCODE ('s','r','c')
const NCode_t	F_STATUS = AMOS_ENCODE ('s','t','s')
const NCode_t	F_TYPE = AMOS_ENCODE ('t','y','p')
const NCode_t	F_VECTORCLEAR = AMOS_ENCODE ('v','c','r')
const NCode_t	M_NULL = AMOS_ENCODE ('N','U','L')
const NCode_t	M_UNIVERSAL = AMOS_ENCODE ('U','N','V')
const NCode_t	M_CONTIG = AMOS_ENCODE ('C','T','G')
const NCode_t	M_CONTIGEDGE = AMOS_ENCODE ('C','T','E')
const NCode_t	M_CONTIGLINK = AMOS_ENCODE ('C','T','L')
const NCode_t	M_DISTRIBUTION = AMOS_ENCODE ('D','S','T')
const NCode_t	M_EDGE = AMOS_ENCODE ('E','D','G')
const NCode_t	M_FEATURE = AMOS_ENCODE ('F','E','A')
const NCode_t	M_FRAGMENT = AMOS_ENCODE ('F','R','G')
const NCode_t	M_GROUP = AMOS_ENCODE ('G','R','P')
const NCode_t	M_KMER = AMOS_ENCODE ('K','M','R')
const NCode_t	M_LAYOUT = AMOS_ENCODE ('L','A','Y')
const NCode_t	M_LIBRARY = AMOS_ENCODE ('L','I','B')
const NCode_t	M_LINK = AMOS_ENCODE ('L','N','K')
const NCode_t	M_IDMAP = AMOS_ENCODE ('M','A','P')
const NCode_t	M_INDEX = AMOS_ENCODE ('I','D','X')
const NCode_t	M_OVERLAP = AMOS_ENCODE ('O','V','L')
const NCode_t	M_READ = AMOS_ENCODE ('R','E','D')
const NCode_t	M_SCAFFOLD = AMOS_ENCODE ('S','C','F')
const NCode_t	M_SCAFFOLDEDGE = AMOS_ENCODE ('S','C','E')
const NCode_t	M_SCAFFOLDLINK = AMOS_ENCODE ('S','C','L')
const NCode_t	M_SEQUENCE = AMOS_ENCODE ('S','E','Q')
const NCode_t	M_TILE = AMOS_ENCODE ('T','L','E')

Typedef Documentation

typedef uint8_t AMOS::BankMode_t

Definition at line 34 of file Bank_AMOS.hh.

typedef std::list<TiledRead_t> AMOS::TiledReadList_t

Definition at line 85 of file ContigIterator_AMOS.hh.

typedef Range_t AMOS::Ordered_Range_t

Definition at line 467 of file datatypes_AMOS.hh.

typedef char AMOS::FeatureType_t

Definition at line 20 of file Feature_AMOS.hh.

typedef char AMOS::FragmentType_t

Definition at line 20 of file Fragment_AMOS.hh.

typedef uint32_t AMOS::ID_t

ID type for iid's.

Definition at line 24 of file inttypes_AMOS.hh.

typedef uint32_t AMOS::NCode_t

unique integer code for dynamic typing

Definition at line 25 of file inttypes_AMOS.hh.

typedef uint32_t AMOS::SD_t

standard deviation type

Definition at line 26 of file inttypes_AMOS.hh.

typedef int32_t AMOS::Size_t

size type (for links,etc)

Definition at line 27 of file inttypes_AMOS.hh.

typedef Size_t AMOS::Pos_t

position type (in a sequence,etc)

Definition at line 28 of file inttypes_AMOS.hh.

typedef char AMOS::Status_t

status type

Definition at line 29 of file inttypes_AMOS.hh.

typedef char AMOS::LinkType_t

Definition at line 21 of file Link_AMOS.hh.

typedef char AMOS::LinkAdjacency_t

Definition at line 22 of file Link_AMOS.hh.

typedef char AMOS::OverlapAdjacency_t

Definition at line 20 of file Overlap_AMOS.hh.

typedef char AMOS::ReadType_t

Definition at line 21 of file Read_AMOS.hh.

Function Documentation

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

Definition at line 1061 of file Bank_AMOS.cc.

References Decode(), and AMOS::Bank_t::IFO_STORE_SUFFIX.

void AMOS::PrintBankVersion ( const char * s )

Prints the bank version a program is compatible with.

Parameters:

The program name

Returns:: void

Definition at line 1072 of file Bank_AMOS.cc.

References AMOS::Bank_t::BANK_VERSION.

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

Range_t AMOS::operator &	(	Range_t	a,
		Range_t	b
	)

An intersection operator for Ranges.

Returns the (foward) intersection of two overlapping ranges.

Parameters:

	a	Range A
	b	Range B

Returns:: The intersection of Range A and B or [0,0) if no overlap

Definition at line 247 of file datatypes_AMOS.cc.

Range_t AMOS::operator\|	(	Range_t	a,
		Range_t	b
	)

A union operator for Ranges.

Returns the union of two overlapping ranges

Parameters:

	a	Range A
	b	Range B

Returns:: The union of Range A and B or [0,0) if no overlap

Definition at line 273 of file datatypes_AMOS.cc.

bool AMOS::operator==	(	const Range_t &	a,
		const Range_t &	b
	)

An equality operator for Ranges.

Returns true if the two ranges have equal begin and end values.

Parameters:

	a	Range A
	b	Range B

Returns:: true if a.begin == b.begin && a.end == b.end, else false

Definition at line 298 of file datatypes_AMOS.cc.

bool AMOS::operator!=	(	const Range_t &	a,
		const Range_t &	b
	)

Definition at line 302 of file datatypes_AMOS.cc.

bool AMOS::operator==	(	const Distribution_t &	a,
		const Distribution_t &	b
	)

An equality operator for Distributions.

Returns true if distributions have identical values

Parameters:

	a	Distribution A
	b	Distribution B

Returns:: true if distributions have identical values

Definition at line 309 of file datatypes_AMOS.cc.

bool AMOS::operator!=	(	const Distribution_t &	a,
		const Distribution_t &	b
	)

Definition at line 314 of file datatypes_AMOS.cc.

bool AMOS::operator==	(	const Tile_t &	a,
		const Tile_t &	b
	)

An equality operator for Tiles.

Returns true if distributions have identical values

Parameters:

	a	Tile A
	b	Tile B

Returns:: true if distributions have identical values

Definition at line 321 of file datatypes_AMOS.cc.

bool AMOS::operator!=	(	const Tile_t &	a,
		const Tile_t &	b
	)

Definition at line 328 of file datatypes_AMOS.cc.

void AMOS::WrapString	(	ostream &	out,
		const string &	s,
		int	per
	)

Definition at line 335 of file datatypes_AMOS.cc.

Referenced by operator<<().

void AMOS::WrapString	(	std::ostream &	out,
		const std::string &	s,
		int	per
	)

Inserts a newline every 'per' characters when writing to stream.

std::ostream& AMOS::operator<<	(	std::ostream &	out,
		const Exception_t &	e
	)			`[inline]`

Dump Exception_t info to an ostream.

Definition at line 251 of file exceptions_AMOS.hh.

std::ostream& AMOS::operator<<	(	std::ostream &	out,
		const std::exception &	e
	)			`[inline]`

Dump exception info to an ostream.

Definition at line 263 of file exceptions_AMOS.hh.

char AMOS::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 MIN_QUALITY.

Referenced by AMOS::Sequence_t::uncompress().

uint8_t AMOS::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 MIN_QUALITY.

Referenced by AMOS::Sequence_t::compress().

std::string AMOS::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.

Referenced by BankExists(), AMOS::Message_t::getField(), main(), AMOS::BankStreamSet_t::operator[](), AMOS::BankSet_t::operator[](), AMOS::UniversalSet_t::operator[](), AMOS::Bank_t::syncIFO(), 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 AMOS::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.

Referenced by 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(), and AMOS::Message_t::setMessageCode().

ostream& AMOS::operator<<	(	ostream &	out,
		Read_t &	read
	)

Definition at line 282 of file Read_AMOS.cc.

References AMOS::Range_t::begin, AMOS::Range_t::end, AMOS::Read_t::getClearRange(), AMOS::Universal_t::getComment(), AMOS::IBankable_t::getIID(), AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), and WrapString().

std::ostream& AMOS::operator<<	(	std::ostream &	o,
		Read_t &	read
	)

Dump read object to ostream.

char AMOS::Complement ( char ch )

Returns the DNA complement of an IUPAC character.

Complement-able IUPAC characters are ACGTUMRWSYKVHDB, while NX*- are also acceptable but are self-complementary. Characters other than these will throw an exception.

Parameters:

The character to take the complement of

Exceptions:

ArgumentException_t

if ch is an invalid character

Returns:: void

Definition at line 39 of file utility_AMOS.cc.

References COMPLEMENT_DNA.

void AMOS::ReverseComplement ( string & str )

Definition at line 46 of file utility_AMOS.cc.

References COMPLEMENT_DNA.

Referenced by AMOS::Sequence_t::getSeqString(), AMOS::Contig_t::getUngappedSeqString(), and AMOS::Contig_t::reverseComplement().

void AMOS::ReverseComplement ( char * str )

Takes the DNA reverse complement of an IUPAC string.

Complement-able IUPAC characters are ACGTUMRWSYKVHDB, while NX*- are also acceptable but are self-complementary. Characters other than these will throw an exception.

Parameters:

str

The string to reverse complement

Exceptions:

ArgumentException_t

if invalid characters are found

Returns:: void

Definition at line 62 of file utility_AMOS.cc.

References COMPLEMENT_DNA.

void AMOS::Reverse ( string & str )

Definition at line 78 of file utility_AMOS.cc.

Referenced by AMOS::Sequence_t::getQualString(), and AMOS::Contig_t::getUngappedQualString().

void AMOS::Reverse ( char * str )

Reverses the contents of a string.

Parameters:

str

The string to reverse

Returns:: void

Definition at line 85 of file utility_AMOS.cc.

void* AMOS::SafeCalloc	(	size_t	num,
		size_t	size
	)			`[inline]`

Safe calloc wrapper.

Detects calloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer.

Parameters:

	num	Number of elements to allocate
	size	Number of bytes per element

Postcondition:: The memory is allocated

Exceptions:

AllocException_t

on memory exhaustion

Returns:: Pointer to the new memory block

Definition at line 64 of file utility_AMOS.hh.

References AMOS_THROW_ALLOC.

void* AMOS::SafeMalloc ( size_t size ) [inline]

Safe malloc wrapper.

Detects malloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer.

Parameters:

size

Number of bytes to allocate

Postcondition:: The memory is allocated

Exceptions:

AllocException_t

on memory exhaustion

Returns:: Pointer to the new memory block

Definition at line 85 of file utility_AMOS.hh.

References AMOS_THROW_ALLOC.

Referenced by AMOS::Bank_t::BankPartition_t::BankPartition_t(), and AMOS::Bank_t::concat().

void* AMOS::SafeRealloc	(	void *	P,
		size_t	size
	)			`[inline]`

Safe realloc wrapper.

Detects realloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer. This helps prevent memory leaks by preventing the original memory block from being lost when the realloc function returns NULL.

Parameters:

	P	The memory block to re-allocate
	size	Number of bytes to allocate

Postcondition:: The memory is allocated

Exceptions:

AllocException_t

on memory exhaustion

Returns:: Pointer to the new memory block

Definition at line 109 of file utility_AMOS.hh.

References AMOS_THROW_ALLOC.

Referenced by AMOS::Bank_t::concat(), AMOS::Sequence_t::operator=(), AMOS::Kmer_t::operator=(), AMOS::Sequence_t::setSequence(), and AMOS::Sequence_t::uncompress().

char* AMOS::SafeStrdup ( const char * str ) [inline]

Safe strdup wrapper.

Detects malloc failure and throws AMOS::AllocException_t exception instead of returning a NULL pointer.

Parameters:

str

The string to copy

Postcondition:: The memory is allocated and the string is copied

Exceptions:

AllocException_t

on memory exhaustion

Returns:: Pointer to the new string copy

Definition at line 130 of file utility_AMOS.hh.

References AMOS_THROW_ALLOC.

void AMOS::ReverseComplement ( std::string & str )

Takes the DNA reverse complement of an IUPAC string.

Complement-able IUPAC characters are ACGTUMRWSYKVHDB, while NX*- are also acceptable but are self-complementary. Characters other than these will throw an exception.

Parameters:

str

The string to reverse complement

Exceptions:

ArgumentException_t

if invalid characters are found