AMOS::Link_t

AMOS::Link_t Class Reference

Linking information between two nodes, such as between contigs. More...

#include <Link_AMOS.hh>

Inheritance diagram for AMOS::Link_t:

[legend]
Collaboration diagram for AMOS::Link_t:
[legend]
List of all members.

Public Member Functions

 Link_t ()
 Constructs an empty Link_t object.
 Link_t (const Link_t &source)
 Copy constructor.
 ~Link_t ()
 Destroys a Link_t object.
virtual void clear ()
 Clears all object data, reinitializes the 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.
virtual NCode_t getNCode () const
 Get the AMOS NCode type identifier.
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.
NCode_t getNodeType () const
 Get the node type.
LinkType_t getType () const
 Get the link type.
virtual void readMessage (const Message_t &msg)
 Reads in data from a Message object.
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 setNodeType (NCode_t nodtype)
 Set the type of node.
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.
virtual void writeMessage (Message_t &msg) const
 Writes data to a Message object.
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_LINK
 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

Detailed Description

Linking information between two nodes, such as between contigs.

A single piece of linking information between two nodes. For example, a probable extension of this class would be a ContigLink_t to represent an inferred relationship between two contigs. These atomic links can be bundled together to form an Edge_t.

Definition at line 33 of file Link_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Link_t::Link_t (  )  [inline]

Constructs an empty Link_t object.

Sets all members to zero or NULL

Definition at line 93 of file Link_AMOS.hh.

References AMOS::NULL_ID, NULL_LINK, and AMOS::NULL_NCODE.

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

Copy constructor.

Definition at line 106 of file Link_AMOS.hh.

AMOS::Link_t::~Link_t (  )  [inline]

Destroys a Link_t object.

Definition at line 115 of file Link_AMOS.hh.

Member Function Documentation

void Link_t::clear (  )  [virtual]

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

Definition at line 22 of file Link_AMOS.cc.

References AMOS::Universal_t::clear(), AMOS::NULL_ID, NULL_LINK, and AMOS::NULL_NCODE.

Referenced by AMOS::ScaffoldLink_t::clear(), AMOS::Edge_t::clear(), AMOS::ContigLink_t::clear(), readMessage(), and writeMessage().

void Link_t::flip (  ) 

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 ANTINORMAL, getAdjacency(), NORMAL, and setAdjacency().

LinkAdjacency_t Link_t::getAdjacency (  )  const

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

Referenced by flip(), and 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<<().

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::Link_t::getNCode (  )  const [inline, virtual]

Get the AMOS NCode type identifier.

Returns:
The AMOS NCode type identifier

Reimplemented from AMOS::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

Definition at line 165 of file Link_AMOS.hh.

References NCODE.

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

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 AMOS::ContigLink_t::getContigs(), and AMOS::ScaffoldLink_t::getScaffolds().

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

Get the node type.

Describes the type of IID the nodes represent.

Returns:
The node type

Reimplemented in AMOS::ContigLink_t, and AMOS::ScaffoldLink_t.

Definition at line 215 of file Link_AMOS.hh.

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

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]

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]

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]

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 Link_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::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

Definition at line 64 of file Link_AMOS.cc.

References AMOS_THROW_ARGUMENT, clear(), AMOS::Encode(), AMOS::F_ADJACENCY, AMOS::F_NODES, AMOS::F_OBJECT, AMOS::F_SD, AMOS::F_SIZE, AMOS::F_SOURCE, AMOS::F_TYPE, AMOS::NCODE_SIZE, AMOS::Universal_t::readMessage(), setAdjacency(), and setType().

Referenced by AMOS::ScaffoldLink_t::readMessage(), AMOS::Edge_t::readMessage(), and AMOS::ContigLink_t::readMessage().

virtual void AMOS::Link_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::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

virtual void AMOS::Link_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::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

void Link_t::setAdjacency ( LinkAdjacency_t  adj  ) 

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

Referenced by flip(), and 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::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]

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 AMOS::ContigLink_t::setContigs(), and AMOS::ScaffoldLink_t::setScaffolds().

void AMOS::Link_t::setNodeType ( NCode_t  nodtype  )  [inline]

Set the type of node.

Describes the type of IID the nodes represent.

Parameters:
nodtype The new node type
Returns:
void

Definition at line 281 of file Link_AMOS.hh.

Referenced by AMOS::ScaffoldLink_t::readMessage(), and AMOS::ContigLink_t::readMessage().

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

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]

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]

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  ) 

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 ALIGNMENT, AMOS_THROW_ARGUMENT, MATEPAIR, NULL_LINK, OTHER, OVERLAP, PHYSICAL, and SYNTENY.

Referenced by readMessage().

void Link_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::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

Definition at line 226 of file Link_AMOS.cc.

References clear(), AMOS::Decode(), AMOS::F_ADJACENCY, AMOS::F_NODES, AMOS::F_OBJECT, AMOS::F_SD, AMOS::F_SIZE, AMOS::F_SOURCE, AMOS::F_TYPE, getAdjacency(), NCODE, NULL_ADJACENCY, AMOS::NULL_ID, NULL_LINK, AMOS::NULL_NCODE, AMOS::NULL_STRING, and AMOS::Universal_t::writeMessage().

Referenced by AMOS::ScaffoldLink_t::writeMessage(), AMOS::Edge_t::writeMessage(), and AMOS::ContigLink_t::writeMessage().

virtual void AMOS::Link_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::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

Member Data Documentation

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

adjacency exists flag

Definition at line 48 of file Link_AMOS.hh.

Referenced by getAdjacency(), and setAdjacency().

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

adjacency info mask

Definition at line 49 of file Link_AMOS.hh.

Referenced by getAdjacency(), and setAdjacency().

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

Definition at line 78 of file Link_AMOS.hh.

Referenced by setType().

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

B,E.

Definition at line 83 of file Link_AMOS.hh.

Referenced by flip(), getAdjacency(), and setAdjacency().

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

Definition at line 51 of file Link_AMOS.hh.

Referenced by getAdjacency(), and 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]

bank flags, derived classes may use "nibble"

Definition at line 68 of file Bank_AMOS.hh.

Referenced by AMOS::Bank_t::appendBID(), AMOS::Sequence_t::clear(), AMOS::IBankable_t::clear(), AMOS::Sequence_t::compress(), AMOS::Bank_t::fetchBID(), AMOS::Bank_t::fetchBIDFix(), AMOS::Overlap_t::getAdjacency(), getAdjacency(), AMOS::Sequence_t::isCompressed(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), AMOS::Overlap_t::isFlagC(), AMOS::IBankable_t::isModified(), AMOS::IBankable_t::isRemoved(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Bank_t::replaceBID(), AMOS::Overlap_t::setAdjacency(), setAdjacency(), AMOS::IBankable_t::setFlagA(), AMOS::IBankable_t::setFlagB(), AMOS::Overlap_t::setFlagC(), and AMOS::Sequence_t::uncompress().

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]

E,E.

Definition at line 84 of file Link_AMOS.hh.

Referenced by getAdjacency(), and setAdjacency().

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

Definition at line 52 of file Link_AMOS.hh.

Referenced by getAdjacency(), and setAdjacency().

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

Definition at line 75 of file Link_AMOS.hh.

Referenced by setType().

const NCode_t Link_t::NCODE = M_LINK [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Universal_t.

Reimplemented in AMOS::ContigEdge_t, AMOS::ContigLink_t, AMOS::Edge_t, AMOS::ScaffoldEdge_t, and AMOS::ScaffoldLink_t.

Definition at line 71 of file Link_AMOS.hh.

Referenced by getNCode(), and writeMessage().

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

E,B.

Definition at line 82 of file Link_AMOS.hh.

Referenced by flip(), getAdjacency(), and setAdjacency().

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

Definition at line 50 of file Link_AMOS.hh.

Referenced by getAdjacency(), and setAdjacency().

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

Definition at line 81 of file Link_AMOS.hh.

Referenced by getAdjacency(), setAdjacency(), and writeMessage().

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

Definition at line 73 of file Link_AMOS.hh.

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

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

Definition at line 74 of file Link_AMOS.hh.

Referenced by setType().

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

B,B.

Definition at line 85 of file Link_AMOS.hh.

Referenced by getAdjacency(), and setAdjacency().

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

Definition at line 53 of file Link_AMOS.hh.

Referenced by getAdjacency(), and setAdjacency().

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

Definition at line 76 of file Link_AMOS.hh.

Referenced by setType().

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

Definition at line 77 of file Link_AMOS.hh.

Referenced by setType().

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

Definition at line 79 of file Link_AMOS.hh.

Referenced by setType().

The documentation for this class was generated from the following files:
Generated on Mon Feb 22 17:36:37 2010 for libAMOS by  doxygen 1.4.7