libAMOS: AMOS::ContigLink_t Class Reference

AMOS::ContigLink_t::ContigLink_t ( ) [inline]

Constructs an empty ContigLink_t object.

Sets all members to zero or NULL

Definition at line 64 of file ContigLink_AMOS.hh.

AMOS::ContigLink_t::ContigLink_t ( const ContigLink_t & source ) [inline]

Copy constructor.

Definition at line 73 of file ContigLink_AMOS.hh.

AMOS::ContigLink_t::~ContigLink_t ( ) [inline]

Destroys a ContigLink_t object.

Definition at line 82 of file ContigLink_AMOS.hh.

virtual void AMOS::ContigLink_t::clear ( ) [inline, virtual]

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

Definition at line 89 of file ContigLink_AMOS.hh.

References AMOS::Link_t::clear().

Referenced by AMOS::ContigEdge_t::clear(), readMessage(), and writeMessage().

void Link_t::flip ( ) [inherited]

Flip the orientation of the link.

Reverses the order of the IIDs and changes the adjacency as altered by the new orientation of the nodes. Does not alter adjacency if it is currently a NULL_ADJACENCY. After flip, NORMAL become ANTINORMAL, ANTINORMAL becomes NORMAL, and INNIE and OUTIE remain the same.

Returns:: void

Definition at line 34 of file Link_AMOS.cc.

References AMOS::Link_t::ANTINORMAL, AMOS::Link_t::getAdjacency(), AMOS::Link_t::NORMAL, and AMOS::Link_t::setAdjacency().

LinkAdjacency_t Link_t::getAdjacency ( ) const [inherited]

Get the adjacency relation of the two nodes.

Get the adjacency information for the nodes, i.e. [N]ORMAL (EB), [A]NTINORMAL (BE), [I]NNIE (EE) or [O]UTIE (BB). Where, if we picture each node as an arrow, B is the tail and E is the head. Thus EB means the head of node1 is adjacent to the tail of node2. This may seem awkward in a theoretical sense, but comes in handy when the nodes are directed sequences.

Returns:: The pair of adjacent ends

Definition at line 47 of file Link_AMOS.cc.

References AMOS::Link_t::ADJACENCY_BIT, AMOS::Link_t::ADJACENCY_BITS, AMOS::Link_t::ANTINORMAL, AMOS::Link_t::ANTINORMAL_BITS, AMOS::IBankable_t::flags_m, AMOS::Link_t::INNIE, AMOS::Link_t::INNIE_BITS, AMOS::Link_t::NORMAL, AMOS::Link_t::NORMAL_BITS, AMOS::Link_t::NULL_ADJACENCY, AMOS::Link_t::OUTIE, and AMOS::Link_t::OUTIE_BITS.

Referenced by AMOS::Link_t::flip(), and AMOS::Link_t::writeMessage().

const std::string& AMOS::Universal_t::getComment ( ) const [inline, inherited]

Get the comment string.

Returns:: The comment string

Definition at line 116 of file Universal_AMOS.hh.

Referenced by AMOS::operator<<().

std::pair<ID_t, ID_t> AMOS::ContigLink_t::getContigs ( ) const [inline]

Get the pair of contig IIDs joined by this link.

Returns:: The first and second contig IIDs joined by this link

Definition at line 100 of file ContigLink_AMOS.hh.

References AMOS::Link_t::getNodes().

const std::string& AMOS::IBankable_t::getEID ( ) const [inline, inherited]

Get the external ID.

Returns:: The external ID

Definition at line 174 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m.

Referenced by AMOS::TiledRead_t::TiledRead_t().

ID_t AMOS::IBankable_t::getIID ( ) const [inline, inherited]

Get the internal ID.

Returns:: The internal ID

Definition at line 185 of file Bank_AMOS.hh.

References AMOS::IBankable_t::iid_m.

Referenced by AMOS::Index_t::buildContigFeature(), AMOS::Index_t::buildContigScaffold(), AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildScaffoldFeature(), and AMOS::operator<<().

virtual NCode_t AMOS::ContigLink_t::getNCode ( ) const [inline, virtual]

Get the AMOS NCode type identifier.

Returns:: The AMOS NCode type identifier

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

Definition at line 107 of file ContigLink_AMOS.hh.

References NCODE.

std::pair<ID_t, ID_t> AMOS::Link_t::getNodes ( ) const [inline, inherited]

Get the pair of node IIDs joined by this link.

Returns:: The first and second node IIDs joined by this link

Definition at line 158 of file Link_AMOS.hh.

Referenced by getContigs(), and AMOS::ScaffoldLink_t::getScaffolds().

NCode_t AMOS::ContigLink_t::getNodeType ( ) const [inline]

Get the node type.

Describes the type of IID the nodes represent.

Returns:: The node type

Reimplemented from AMOS::Link_t.

Definition at line 114 of file ContigLink_AMOS.hh.

References AMOS::Contig_t::NCODE.

SD_t AMOS::Link_t::getSD ( ) const [inline, inherited]

Get the standard deviation of the link size.

Returns:: The standard deviation of the link

Definition at line 176 of file Link_AMOS.hh.

Size_t AMOS::Link_t::getSize ( ) const [inline, inherited]

Get the weight/size of the link.

Returns:: The weight/size of the link

Definition at line 187 of file Link_AMOS.hh.

std::pair<ID_t, NCode_t> AMOS::Link_t::getSource ( ) const [inline, inherited]

Get the link source IID and type.

This method only returns the IID of the link source and the object type. The entire source object can be obtained by fetching the specified IID from the corresponding bank.

Returns:: The IID of the link source and the NCode type indentifier

Definition at line 202 of file Link_AMOS.hh.

const Status_t AMOS::Universal_t::getStatus ( ) const [inline, inherited]

Get the status value.

Returns:: The status value

Definition at line 127 of file Universal_AMOS.hh.

LinkType_t AMOS::Link_t::getType ( ) const [inline, inherited]

Get the link type.

Describes the type of link this object represents.

Returns:: The type of link

Definition at line 228 of file Link_AMOS.hh.

bool AMOS::IBankable_t::isFlagA ( ) const [inline, inherited]

Check the value of flag A.

Returns:: The value of flag A

Definition at line 228 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isFlagB ( ) const [inline, inherited]

Check the value of flag B.

Returns:: The value of flag B

Definition at line 239 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isModified ( ) const [inline, inherited]

Check if the object has been modified.

Returns:: true if modified, otherwise false

Definition at line 217 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

bool AMOS::IBankable_t::isRemoved ( ) const [inline, inherited]

Check if the object is waiting to be removed from the bank.

Note:: Useful for debugging only

Returns:: true if removed, otherwise false

Definition at line 206 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

void ContigLink_t::readMessage ( const Message_t & msg ) [virtual]

Reads in data from a Message object.

Reads the data contained in a Message object and stores it in the Messagable object. Will not complain if incoming message is of the wrong type, will only try and suck out the fields it recognizes. All previous data in the Messagable object will be cleared or overwritten.

Parameters:

msg

The Message to read from

Precondition:: The expected fields are formatted properly

Exceptions:

ArgumentException_t

Returns:: void

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

Definition at line 22 of file ContigLink_AMOS.cc.

References clear(), AMOS::NULL_NCODE, AMOS::Link_t::readMessage(), and AMOS::Link_t::setNodeType().

Referenced by AMOS::ContigEdge_t::readMessage().

virtual void AMOS::ContigLink_t::readRecord	(	std::istream &	fix,
		std::istream &	var
	)			`[protected, virtual]`

Read selected class members from a biserial record.

Reads the fixed and variable length streams from a biserial record and initializes the class members to the values stored within. Used in translating a biserial IBankable object, and needed to retrieve objects from a bank.

Note:: This method must be able to interpret the biserial record produced by its related function writeRecord.

Parameters:

	fix	The fixed length stream (stores all fixed length members)
	var	The variable length stream (stores all var length members)

Precondition:: The get pointer of fix is at the beginning of the record
The get pointer of var is at the beginning of the record

Returns:: void

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

virtual void AMOS::ContigLink_t::readRecordFix ( std::istream & fix ) [protected, virtual]

Read selected class members from a fixed store only.

Reads the fixed stream and initializes the class members to the values stored within. Used to fetch the fixed portion of a biserial IBankable object, and needed to retrieve objects from a bank.

Note:: This method must be able to interpret the biserial record produced by its related function writeRecord.

Parameters:

fix

The fixed length stream (stores all fixed length members)

Precondition:: The get pointer of fix is at the beginning of the record

Returns:: void

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

void Link_t::setAdjacency ( LinkAdjacency_t adj ) [inherited]

Set the adjacent ends of the two nodes.

Set the adjacency information for the nodes, i.e. [N]ORMAL (EB), [A]NTINORMAL (BE), [I]NNIE (EE) or [O]UTIE (BB). Where, if we picture each node as an arrow, B is the tail and E is the head. Thus EB means the head of node1 is adjacent to the tail of node2. This may seem awkward in a theoretical sense, but comes in handy when the nodes are directed sequences.

Note:: Will store info in nibble portion of BankFlags

Parameters:

adj

The new adjacency of the nodes

Precondition:: adj must be one of [NAIO]

Exceptions:

ArgumentException_t

Returns:: void

Definition at line 182 of file Link_AMOS.cc.

References AMOS::Link_t::ADJACENCY_BIT, AMOS::Link_t::ADJACENCY_BITS, AMOS_THROW_ARGUMENT, AMOS::Link_t::ANTINORMAL, AMOS::Link_t::ANTINORMAL_BITS, AMOS::IBankable_t::flags_m, AMOS::Link_t::INNIE, AMOS::Link_t::INNIE_BITS, AMOS::Link_t::NORMAL, AMOS::Link_t::NORMAL_BITS, AMOS::Link_t::NULL_ADJACENCY, AMOS::Link_t::OUTIE, and AMOS::Link_t::OUTIE_BITS.

Referenced by AMOS::Link_t::flip(), and AMOS::Link_t::readMessage().

void AMOS::Universal_t::setComment ( const std::string & comment ) [inline, inherited]

Set the comment string.

Parameters:

comment

The new comment string

Returns:: void

Definition at line 150 of file Universal_AMOS.hh.

void AMOS::ContigLink_t::setContigs ( std::pair< ID_t, ID_t > contigs ) [inline]

Set the contig IID pair for this link.

Only returns the IIDs of the contigs. It is up to the user to keep track of where the actual contig objects are stored.

Parameters:

contigs

The new pair of contig IIDs

Returns:: void

Definition at line 133 of file ContigLink_AMOS.hh.

References AMOS::Link_t::setNodes().

void AMOS::IBankable_t::setEID ( const std::string & eid ) [inline, inherited]

Set the external ID.

Will only use the characters up to but not including the first newline.

Returns:: void

Definition at line 252 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m, and AMOS::NL_CHAR.

void AMOS::IBankable_t::setFlagA ( bool flag ) [inline, inherited]

Set flag A.

Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag B.

Parameters:

flag

The new flag A value

Returns:: void

Definition at line 272 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::IBankable_t::setFlagB ( bool flag ) [inline, inherited]

Set flag B.

Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag A.

Parameters:

flag

The new flag B value

Returns:: void

Definition at line 288 of file Bank_AMOS.hh.

References AMOS::IBankable_t::flags_m.

Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::IBankable_t::setIID ( ID_t iid ) [inline, inherited]

Set the internal ID.

Parameters:

iid

The new internal ID

Returns:: void

Definition at line 300 of file Bank_AMOS.hh.

References AMOS::IBankable_t::iid_m.

void AMOS::Link_t::setNodes ( std::pair< ID_t, ID_t > nods ) [inline, inherited]

Set the node IID pair for this link.

Only returns the IIDs of the nodes. It is up to the user to keep track of where the actual node objects are stored.

Parameters:

nods

The new pair of node IIDs

Returns:: void

Definition at line 267 of file Link_AMOS.hh.

Referenced by setContigs(), and AMOS::ScaffoldLink_t::setScaffolds().

void AMOS::Link_t::setSD ( SD_t sd ) [inline, inherited]

Set the standard deviation of the link size.

Parameters:

sd

The new standard deviation for the link size

Returns:: void

Definition at line 293 of file Link_AMOS.hh.

void AMOS::Link_t::setSize ( Size_t size ) [inline, inherited]

Set the weight/size of the link.

Parameters:

size

The new link weight/size

Returns:: void

Definition at line 305 of file Link_AMOS.hh.

void AMOS::Link_t::setSource ( std::pair< ID_t, NCode_t > source ) [inline, inherited]

Set the link source IID.

Parameters:

source

The new IID and NCode type identifier of the link source

Returns:: void

Definition at line 317 of file Link_AMOS.hh.

void AMOS::Universal_t::setStatus ( Status_t status ) [inline, inherited]

Set the status value.

Parameters:

status

The new status value

Returns:: void

Definition at line 162 of file Universal_AMOS.hh.

Referenced by AMOS::Universal_t::readMessage().

void Link_t::setType ( LinkType_t type ) [inherited]

Set the linking type.

Parameters:

type

The new link type

Precondition:: type is one of [XMOPAS] or NULL

Exceptions:

ArgumentException_t

Returns:: void

Definition at line 205 of file Link_AMOS.cc.

References AMOS::Link_t::ALIGNMENT, AMOS_THROW_ARGUMENT, AMOS::Link_t::MATEPAIR, AMOS::Link_t::NULL_LINK, AMOS::Link_t::OTHER, AMOS::Link_t::OVERLAP, AMOS::Link_t::PHYSICAL, and AMOS::Link_t::SYNTENY.

Referenced by AMOS::Link_t::readMessage().

void ContigLink_t::writeMessage ( Message_t & msg ) const [virtual]

Writes data to a Message object.

Writes the data contained in a Messagable object to a Message object. All previous data in the Message will be cleared or overwritten.

Parameters:

msg

The Message to write to

Returns:: void

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

Definition at line 57 of file ContigLink_AMOS.cc.

References clear(), NCODE, and AMOS::Link_t::writeMessage().

Referenced by AMOS::ContigEdge_t::writeMessage().

virtual void AMOS::ContigLink_t::writeRecord	(	std::ostream &	fix,
		std::ostream &	var
	)			const `[protected, virtual]`

Write selected class members to a biserial record.

Writes the fixed and variable length streams to a biserial record. Used in generating a biserial IBankable object, and needed to commit objects to a bank. Should not write the flags, EID, or IID of the object because the bank will handle the storage of these fields on its own.

Note:: This method must be able to produce a biserial record that can be read by its related funtion readRecord.

Parameters:

	fix	The fixed length stream (stores all fixed length members)
	var	The variable length stream (stores all var length members)

Returns:: void

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

const uint8_t AMOS::Link_t::ADJACENCY_BIT = 0x4 [static, protected, inherited]

adjacency exists flag

Definition at line 48 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const uint8_t AMOS::Link_t::ADJACENCY_BITS = 0x3 [static, protected, inherited]

adjacency info mask

Definition at line 49 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const LinkType_t AMOS::Link_t::ALIGNMENT = 'A' [static, inherited]

Definition at line 78 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::setType().

const LinkAdjacency_t AMOS::Link_t::ANTINORMAL = 'A' [static, inherited]

B,E.

Definition at line 83 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::flip(), AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const uint8_t AMOS::Link_t::ANTINORMAL_BITS = 0x2 [static, protected, inherited]

Definition at line 51 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

std::string AMOS::IBankable_t::eid_m [protected, inherited]

external ID (anything you want sans newlines)

Definition at line 66 of file Bank_AMOS.hh.

Referenced by AMOS::Bank_t::append(), AMOS::IBankable_t::clear(), AMOS::IBankable_t::getEID(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Universal_t::readMessage(), AMOS::BankStream_t::replace(), AMOS::Bank_t::replace(), AMOS::BankStream_t::replaceByBID(), AMOS::IBankable_t::setEID(), and AMOS::Universal_t::writeMessage().

BankFlags_t AMOS::IBankable_t::flags_m [protected, inherited]

ID_t AMOS::IBankable_t::iid_m [protected, inherited]

internal ID (integer AMOS identifier)

Definition at line 64 of file Bank_AMOS.hh.

Referenced by AMOS::Bank_t::append(), AMOS::IBankable_t::clear(), AMOS::IBankable_t::getIID(), AMOS::IBankable_t::IBankable_t(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Universal_t::readMessage(), AMOS::BankStream_t::replace(), AMOS::Bank_t::replace(), AMOS::BankStream_t::replaceByBID(), AMOS::IBankable_t::setIID(), and AMOS::Universal_t::writeMessage().

const LinkAdjacency_t AMOS::Link_t::INNIE = 'I' [static, inherited]

E,E.

Definition at line 84 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const uint8_t AMOS::Link_t::INNIE_BITS = 0x3 [static, protected, inherited]

Definition at line 52 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const LinkType_t AMOS::Link_t::MATEPAIR = 'M' [static, inherited]

Definition at line 75 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::setType().

const NCode_t ContigLink_t::NCODE = M_CONTIGLINK [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Link_t.

Reimplemented in AMOS::ContigEdge_t.

Definition at line 56 of file ContigLink_AMOS.hh.

Referenced by getNCode(), and writeMessage().

const LinkAdjacency_t AMOS::Link_t::NORMAL = 'N' [static, inherited]

E,B.

Definition at line 82 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::flip(), AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const uint8_t AMOS::Link_t::NORMAL_BITS = 0x1 [static, protected, inherited]

Definition at line 50 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const LinkAdjacency_t AMOS::Link_t::NULL_ADJACENCY = 0 [static, inherited]

Definition at line 81 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), AMOS::Link_t::setAdjacency(), and AMOS::Link_t::writeMessage().

const LinkType_t AMOS::Link_t::NULL_LINK = 0 [static, inherited]

Definition at line 73 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::clear(), AMOS::Link_t::Link_t(), AMOS::Link_t::setType(), and AMOS::Link_t::writeMessage().

const LinkType_t AMOS::Link_t::OTHER = 'X' [static, inherited]

Definition at line 74 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::setType().

const LinkAdjacency_t AMOS::Link_t::OUTIE = 'O' [static, inherited]

B,B.

Definition at line 85 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const uint8_t AMOS::Link_t::OUTIE_BITS = 0x0 [static, protected, inherited]

Definition at line 53 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::getAdjacency(), and AMOS::Link_t::setAdjacency().

const LinkType_t AMOS::Link_t::OVERLAP = 'O' [static, inherited]

Definition at line 76 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::setType().

const LinkType_t AMOS::Link_t::PHYSICAL = 'P' [static, inherited]

Definition at line 77 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::setType().

const LinkType_t AMOS::Link_t::SYNTENY = 'S' [static, inherited]

Definition at line 79 of file Link_AMOS.hh.

Referenced by AMOS::Link_t::setType().

AMOS::ContigLink_t Class Reference

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation


Public Member Functions
	ContigLink_t ()
	Constructs an empty ContigLink_t object.
	ContigLink_t (const ContigLink_t &source)
	Copy constructor.
	~ContigLink_t ()
	Destroys a ContigLink_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
std::pair< ID_t, ID_t >	getContigs () const
	Get the pair of contig IIDs joined by this link.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
NCode_t	getNodeType () const
	Get the node type.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setContigs (std::pair< ID_t, ID_t > contigs)
	Set the contig IID pair for this link.
virtual void	writeMessage (Message_t &msg) const
	Writes data to a Message object.
void	flip ()
	Flip the orientation of the link.
LinkAdjacency_t	getAdjacency () const
	Get the adjacency relation of the two nodes.
std::pair< ID_t, ID_t >	getNodes () const
	Get the pair of node IIDs joined by this link.
SD_t	getSD () const
	Get the standard deviation of the link size.
Size_t	getSize () const
	Get the weight/size of the link.
std::pair< ID_t, NCode_t >	getSource () const
	Get the link source IID and type.
LinkType_t	getType () const
	Get the link type.
void	setAdjacency (LinkAdjacency_t adj)
	Set the adjacent ends of the two nodes.
void	setNodes (std::pair< ID_t, ID_t > nods)
	Set the node IID pair for this link.
void	setSD (SD_t sd)
	Set the standard deviation of the link size.
void	setSize (Size_t size)
	Set the weight/size of the link.
void	setSource (std::pair< ID_t, NCode_t > source)
	Set the link source IID.
void	setType (LinkType_t type)
	Set the linking type.
const std::string &	getComment () const
	Get the comment string.
const Status_t	getStatus () const
	Get the status value.
void	setComment (const std::string &comment)
	Set the comment string.
void	setStatus (Status_t status)
	Set the status value.
const std::string &	getEID () const
	Get the external ID.
ID_t	getIID () const
	Get the internal ID.
bool	isRemoved () const
	Check if the object is waiting to be removed from the bank.
bool	isModified () const
	Check if the object has been modified.
bool	isFlagA () const
	Check the value of flag A.
bool	isFlagB () const
	Check the value of flag B.
void	setEID (const std::string &eid)
	Set the external ID.
void	setFlagA (bool flag)
	Set flag A.
void	setFlagB (bool flag)
	Set flag B.
void	setIID (ID_t iid)
	Set the internal ID.
Static Public Attributes
static const NCode_t	NCODE = M_CONTIGLINK
	The NCode type identifier for this object.
static const LinkType_t	NULL_LINK = 0
static const LinkType_t	OTHER = 'X'
static const LinkType_t	MATEPAIR = 'M'
static const LinkType_t	OVERLAP = 'O'
static const LinkType_t	PHYSICAL = 'P'
static const LinkType_t	ALIGNMENT = 'A'
static const LinkType_t	SYNTENY = 'S'
static const LinkAdjacency_t	NULL_ADJACENCY = 0
static const LinkAdjacency_t	NORMAL = 'N'
	E,B.
static const LinkAdjacency_t	ANTINORMAL = 'A'
	B,E.
static const LinkAdjacency_t	INNIE = 'I'
	E,E.
static const LinkAdjacency_t	OUTIE = 'O'
	B,B.
Protected Member Functions
virtual void	readRecord (std::istream &fix, std::istream &var)
	Read selected class members from a biserial record.
virtual void	readRecordFix (std::istream &fix)
	Read selected class members from a fixed store only.
virtual void	writeRecord (std::ostream &fix, std::ostream &var) const
	Write selected class members to a biserial record.
Protected Attributes
ID_t	iid_m
	internal ID (integer AMOS identifier)
std::string	eid_m
	external ID (anything you want sans newlines)
BankFlags_t	flags_m
	bank flags, derived classes may use "nibble"
Static Protected Attributes
static const uint8_t	ADJACENCY_BIT = 0x4
	adjacency exists flag
static const uint8_t	ADJACENCY_BITS = 0x3
	adjacency info mask
static const uint8_t	NORMAL_BITS = 0x1
static const uint8_t	ANTINORMAL_BITS = 0x2
static const uint8_t	INNIE_BITS = 0x3
static const uint8_t	OUTIE_BITS = 0x0