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AMOS Namespace Reference

Compounds
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	Bank_t
	An AMOS data bank for efficiently storing Bankable data types. More...
class	BankPartition_t
	A single partition of the file-based Bank. More...
class	Contig_t
	A tiling of assembled sequence reads. More...
class	ContigEdge_t
	Reliable linking information between two contigs. More...
class	ContigLink_t
	Linking information between two contigs. More...
struct	Distribution_t
	A set of statistics that define a distribution. More...
class	Example_t
	Minimal set of IBankable members. More...
class	Exception_t
	The base AMOS excpetion class. More...
class	Fragment_t
	Single piece of DNA. More...
struct	HashNode_t
	HashNode for IDMap. More...
struct	BankableFlags_t
	8 bit flag set for IBankable types More...
class	IBankable_t
	Interface for classes that can be stored in an AMOS Bank. More...
class	IDMap_t
	A one-to-one mapping of IDs. More...
class	IMessagable_t
	Interface for classes that can interpret messages. More...
class	IOException_t
	An exception for IO errors. More...
class	Kmer_t
	String of K bases present in the assembly. More...
class	Library_t
	A collection of cloned, size-controlled DNA molecules. More...
class	Matepair_t
	Matepair information for two reads. More...
class	Message_t
	A generic AMOS message object for reading and writing data. More...
class	Overlap_t
	An overlap relation between to sequencing reads. More...
struct	Range_t
	A gapped coordinate range. More...
class	Read_t
	A DNA sequencing read. More...
class	Scaffold_t
	A ordered, oriented and positioned list of contigs. More...
class	Sequence_t
	Sequence bases with quality scores. More...
struct	Tile_t
	A singe sequence's location and orientation in a larger sequence. More...
class	Universal_t
	A universal base class that can be used by Banks or Messages. More...
Typedefs
typedef char	LinkType_t
typedef char	LinkAdjacency_t
typedef Range_t	Ordered_Range_t
typedef char	FragmentType_t
typedef char	MateType_t
typedef char	OverlapAdjacency_t
typedef char	ReadType_t
Functions
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 (std::ostream &out, const std::string &s, int per)
	Inserts a newline every 'per' characters when writing to stream.
std::ostream &	operator<< (std::ostream &o, Exception_t &e)
	Dump Exception_t info to an ostream.
std::ostream &	operator<< (std::ostream &o, std::exception &e)
	Dump exception info to an ostream.
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.
std::ostream &	operator<< (std::ostream &o, Read_t &read)
	Dump read object to ostream.
Variables
const uint8_t	NCODE = 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 char	MIN_QUALITY = '0'
	min quality score definition
const char	MAX_QUALITY = '0' + 63
	max quality score definition

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Typedef Documentation

typedef char AMOS::FragmentType_t

typedef char AMOS::LinkAdjacency_t

typedef char AMOS::LinkType_t

typedef char AMOS::MateType_t

typedef Range_t AMOS::Ordered_Range_t

typedef char AMOS::OverlapAdjacency_t

typedef char AMOS::ReadType_t

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Function Documentation

string AMOS::Decode (  NCode_t    ncode )

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

NCode_t AMOS::Encode (  const std::string &    str )

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( ) == 3 Exceptions: ArgumentException_t  Returns: NCode of the string, or NULL_NCODE if invalid string length

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

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

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

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

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

Dump read object to ostream.

ostream & AMOS::operator<< (  std::ostream &    o, std::exception &    e )

Dump exception info to an ostream.

ostream & AMOS::operator<< (  std::ostream &    o, Exception_t &    e )

Dump Exception_t info to an ostream.

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

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

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

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

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

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

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Variable Documentation

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

max quality score definition

const char AMOS::MIN_QUALITY = '0'

min quality score definition

const uint8_t AMOS::NCODE = 3

length of the NCode strings

const ID_t AMOS::NULL_ID = 0

NULL ID definition.

const NCode_t AMOS::NULL_NCODE = 0

NULL NCode definition.

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