AMOS::ContigEdge_t Class Reference

Reliable linking information between two contigs. More...

#include <ContigEdge_AMOS.hh>

Inheritance diagram for AMOS::ContigEdge_t:

[legend]Collaboration diagram for AMOS::ContigEdge_t:

[legend]List of all members.


Public Member Functions
	ContigEdge_t ()
	Constructs an empty ContigEdge_t object.
	ContigEdge_t (const ContigEdge_t &source)
	Copy constructor.
	~ContigEdge_t ()
	Destroys a ContigEdge_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
const std::vector< ID_t > &	getContigLinks () const
	Get the bundle of contig link IIDs that make up this contig edge.
std::vector< ID_t > &	getContigLinks ()
	Get the bundle of contig link IIDs that make up this contig edge.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setContigLinks (const std::vector< ID_t > &links)
	Set the bundle of contig link IIDs that make up this contig edge.
virtual void	writeMessage (Message_t &msg) const
	Writes data to a Message object.
std::pair< ID_t, ID_t >	getContigs () const
	Get the pair of contig IIDs joined by this link.
NCode_t	getNodeType () const
	Get the node type.
void	setContigs (std::pair< ID_t, ID_t > contigs)
	Set the contig IID pair for this link.
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.
const std::vector< ID_t > &	getLinks () const
	Get the bundle of link IIDs that make up this contig edge.
std::vector< ID_t > &	getLinks ()
	Get the bundle of link IIDs that make up this contig edge.
void	setLinks (const std::vector< ID_t > &links)
	Set the bundle of link IIDs that make up this contig edge.
Static Public Attributes
const NCode_t	NCODE = M_CONTIGEDGE
	The NCode type identifier for this object.
const LinkType_t	NULL_LINK = 0
const LinkType_t	OTHER = 'X'
const LinkType_t	MATEPAIR = 'M'
const LinkType_t	OVERLAP = 'O'
const LinkType_t	PHYSICAL = 'P'
const LinkType_t	ALIGNMENT = 'A'
const LinkType_t	SYNTENY = 'S'
const LinkAdjacency_t	NULL_ADJACENCY = 0
const LinkAdjacency_t	NORMAL = 'N'
	E,B.
const LinkAdjacency_t	ANTINORMAL = 'A'
	B,E.
const LinkAdjacency_t	INNIE = 'I'
	E,E.
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	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
const uint8_t	ADJACENCY_BIT = 0x4
	adjacency exists flag
const uint8_t	ADJACENCY_BITS = 0x3
	adjacency info mask
const uint8_t	NORMAL_BITS = 0x1
const uint8_t	ANTINORMAL_BITS = 0x2
const uint8_t	INNIE_BITS = 0x3
const uint8_t	OUTIE_BITS = 0x0

Detailed Description

Reliable linking information between two contigs.

Derived from a ContigLink_t, this class represents a reliable link between two contigs that is usually composed of multiple contig links. A list of contig edges is generally the output contig scaffolding.

Definition at line 30 of file ContigEdge_AMOS.hh.

Constructor & Destructor Documentation

AMOS::ContigEdge_t::ContigEdge_t ( ) [inline]

Constructs an empty ContigEdge_t object.
Definition at line 57 of file ContigEdge_AMOS.hh.

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

Copy constructor.
Definition at line 66 of file ContigEdge_AMOS.hh.

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

Destroys a ContigEdge_t object.
Definition at line 75 of file ContigEdge_AMOS.hh.

Member Function Documentation

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

Clears all object data, reinitializes the object.

Reimplemented from AMOS::ContigLink_t.
Definition at line 82 of file ContigEdge_AMOS.hh.
References AMOS::IEdge_t::clear(), and AMOS::ContigLink_t::clear().
Referenced by 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 46 of file Link_AMOS.cc.
References AMOS::Link_t::ANTINORMAL, AMOS::Link_t::getAdjacency(), AMOS::LinkAdjacency_t, 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 59 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::Link_t::INNIE, AMOS::Link_t::INNIE_BITS, AMOS::LinkAdjacency_t, 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 110 of file Universal_AMOS.hh.
Referenced by AMOS::operator<<().

std::vector<ID_t>& AMOS::ContigEdge_t::getContigLinks ( ) [inline]

Get the bundle of contig link IIDs that make up this contig edge.

Returns:
A vector of contig link IIDs
Definition at line 106 of file ContigEdge_AMOS.hh.
References AMOS::IEdge_t::getLinks().

const std::vector<ID_t>& AMOS::ContigEdge_t::getContigLinks ( ) const [inline]

Get the bundle of contig link IIDs that make up this contig edge.

Returns:
A vector of contig link IIDs
Definition at line 95 of file ContigEdge_AMOS.hh.
References AMOS::IEdge_t::getLinks().

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

Get the pair of contig IIDs joined by this link.

Returns:
The first and second contig IIDs joined by this link
Definition at line 96 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 156 of file Bank_AMOS.hh.
References AMOS::IBankable_t::eid_m.
Referenced by AMOS::Contig_t::writeUMD().

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

Get the internal ID.

Returns:
The internal ID
Definition at line 167 of file Bank_AMOS.hh.
References AMOS::ID_t, and 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<<().

std::vector<ID_t>& AMOS::IEdge_t::getLinks ( ) [inline, inherited]

Get the bundle of link IIDs that make up this contig edge.

Returns:
A vector of link IIDs
Definition at line 95 of file Edge_AMOS.hh.

const std::vector<ID_t>& AMOS::IEdge_t::getLinks ( ) const [inline, inherited]

Get the bundle of link IIDs that make up this contig edge.

Returns:
A vector of link IIDs
Definition at line 84 of file Edge_AMOS.hh.
Referenced by getContigLinks(), and AMOS::ScaffoldEdge_t::getScaffoldLinks().

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

Get the AMOS NCode type identifier.

Returns:
The AMOS NCode type identifier

Reimplemented from AMOS::ContigLink_t.
Definition at line 113 of file ContigEdge_AMOS.hh.
References AMOS::NCode_t.

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 154 of file Link_AMOS.hh.
References AMOS::ID_t.
Referenced by AMOS::ContigLink_t::getContigs(), and AMOS::ScaffoldLink_t::getScaffolds().

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

Get the node type.
Describes the type of IID the nodes represent.

Returns:
The node type

Reimplemented from AMOS::Link_t.
Definition at line 110 of file ContigLink_AMOS.hh.
References AMOS::NCode_t.

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 172 of file Link_AMOS.hh.
References AMOS::SD_t.

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 183 of file Link_AMOS.hh.
References AMOS::Size_t.

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 198 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 121 of file Universal_AMOS.hh.
References AMOS::Status_t.

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 224 of file Link_AMOS.hh.
References AMOS::LinkType_t.

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

Check the value of flag A.

Returns:
The value of flag A
Definition at line 210 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 221 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 199 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 188 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.

void ContigEdge_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::ContigLink_t.
Definition at line 22 of file ContigEdge_AMOS.cc.
References clear(), AMOS::IEdge_t::readMessage(), and AMOS::ContigLink_t::readMessage().

void ContigEdge_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::ContigLink_t.
Definition at line 39 of file ContigEdge_AMOS.cc.
References AMOS::IEdge_t::readRecord(), and AMOS::ContigLink_t::readRecord().

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 178 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::Link_t::INNIE, AMOS::Link_t::INNIE_BITS, AMOS::LinkAdjacency_t, 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 144 of file Universal_AMOS.hh.

void AMOS::ContigEdge_t::setContigLinks ( const std::vector< ID_t > & links ) [inline]

Set the bundle of contig link IIDs that make up this contig edge.

Parameters:

links The new vector of contig link IIDs

Returns:
void
Definition at line 129 of file ContigEdge_AMOS.hh.
References AMOS::IEdge_t::setLinks().

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

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 129 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 234 of file Bank_AMOS.hh.
References AMOS::IBankable_t::eid_m, and AMOS::NL_CHAR.
Referenced by AMOS::Contig_t::readUMD().

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 254 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 270 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 282 of file Bank_AMOS.hh.
References AMOS::ID_t, and AMOS::IBankable_t::iid_m.

void AMOS::IEdge_t::setLinks ( const std::vector< ID_t > & links ) [inline, inherited]

Set the bundle of link IIDs that make up this contig edge.

Parameters:

links The new vector of link IIDs

Returns:
void
Definition at line 115 of file Edge_AMOS.hh.
References AMOS::ID_t.
Referenced by setContigLinks(), and AMOS::ScaffoldEdge_t::setScaffoldLinks().

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 263 of file Link_AMOS.hh.
Referenced by AMOS::ContigLink_t::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 289 of file Link_AMOS.hh.
References AMOS::SD_t.

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 301 of file Link_AMOS.hh.
References AMOS::Size_t.

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 313 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 156 of file Universal_AMOS.hh.
References AMOS::Status_t.
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 201 of file Link_AMOS.cc.
References AMOS::Link_t::ALIGNMENT, AMOS_THROW_ARGUMENT, AMOS::LinkType_t, 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 ContigEdge_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::ContigLink_t.
Definition at line 49 of file ContigEdge_AMOS.cc.
References clear(), AMOS::IEdge_t::writeMessage(), and AMOS::ContigLink_t::writeMessage().

void ContigEdge_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::ContigLink_t.
Definition at line 69 of file ContigEdge_AMOS.cc.
References AMOS::IEdge_t::writeRecord(), and AMOS::ContigLink_t::writeRecord().

Member Data Documentation

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 Link_t::ALIGNMENT = 'A' [static, inherited]

Definition at line 24 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::setType().

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

B,E.
Definition at line 28 of file Link_AMOS.cc.
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::IBankable_t::clear(), AMOS::IBankable_t::getEID(), and AMOS::IBankable_t::setEID().

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

bank flags, derived classes may use "nibble"
Definition at line 68 of file Bank_AMOS.hh.
Referenced by AMOS::IBankable_t::clear(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), AMOS::IBankable_t::isModified(), AMOS::IBankable_t::isRemoved(), AMOS::IBankable_t::setFlagA(), and AMOS::IBankable_t::setFlagB().

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::IBankable_t::clear(), AMOS::IBankable_t::getIID(), AMOS::IBankable_t::IBankable_t(), and AMOS::IBankable_t::setIID().

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

E,E.
Definition at line 29 of file Link_AMOS.cc.
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 Link_t::MATEPAIR = 'M' [static, inherited]

Definition at line 21 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::setType().

const NCode_t ContigEdge_t::NCODE = M_CONTIGEDGE [static]

The NCode type identifier for this object.

Reimplemented from AMOS::ContigLink_t.
Definition at line 18 of file ContigEdge_AMOS.cc.

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

E,B.
Definition at line 27 of file Link_AMOS.cc.
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 Link_t::NULL_ADJACENCY = 0 [static, inherited]

Definition at line 26 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::getAdjacency(), AMOS::Link_t::setAdjacency(), and AMOS::Link_t::writeMessage().

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

Definition at line 19 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::clear(), AMOS::Link_t::Link_t(), AMOS::Link_t::setType(), and AMOS::Link_t::writeMessage().

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

Definition at line 20 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::setType().

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

B,B.
Definition at line 30 of file Link_AMOS.cc.
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 Link_t::OVERLAP = 'O' [static, inherited]

Definition at line 22 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::setType().

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

Definition at line 23 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::setType().

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

Definition at line 25 of file Link_AMOS.cc.
Referenced by AMOS::Link_t::setType().

The documentation for this class was generated from the following files:

Generated on Tue May 17 15:19:43 2005 for libAMOS by

1.3.8

AMOS::ContigEdge_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