AMOS::IEdge_t Class Reference

Interface for Edge_t. More...

#include <Edge_AMOS.hh>

Inheritance diagram for AMOS::IEdge_t:

[legend]List of all members.

Public Member Functions
	IEdge_t ()
	Constructs an empty IEdge_t object.
	IEdge_t (const IEdge_t &source)
	Copy constructor.
virtual	~IEdge_t ()
	Destroys a IEdge_t object.
void	clear ()
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.
virtual NCode_t	getNCode () const =0
virtual void	readMessage (const Message_t &msg)
void	setLinks (const std::vector< ID_t > &links)
	Set the bundle of link IIDs that make up this contig edge.
virtual void	writeMessage (Message_t &msg) const
Protected Member Functions
virtual void	readRecord (std::istream &fix, std::istream &var)
virtual void	writeRecord (std::ostream &fix, std::ostream &var) const

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Detailed Description

Interface for Edge_t.

Definition at line 25 of file Edge_AMOS.hh.

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Constructor & Destructor Documentation

AMOS::IEdge_t::IEdge_t (   )  [inline]

Constructs an empty IEdge_t object. Definition at line 48 of file Edge_AMOS.hh.

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

Copy constructor. Definition at line 57 of file Edge_AMOS.hh.

virtual AMOS::IEdge_t::~IEdge_t (   )  [inline, virtual]

Destroys a IEdge_t object. Definition at line 66 of file Edge_AMOS.hh.

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Member Function Documentation

void AMOS::IEdge_t::clear (   )  [inline]

Reimplemented in AMOS::ContigEdge_t, AMOS::Edge_t, and AMOS::ScaffoldEdge_t. Definition at line 73 of file Edge_AMOS.hh. Referenced by AMOS::ScaffoldEdge_t::clear(), AMOS::Edge_t::clear(), AMOS::ContigEdge_t::clear(), readMessage(), and writeMessage().

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

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]

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 AMOS::ContigEdge_t::getContigLinks(), and AMOS::ScaffoldEdge_t::getScaffoldLinks().

virtual NCode_t AMOS::IEdge_t::getNCode (   )  const [pure virtual]

Implemented in AMOS::ContigEdge_t, AMOS::Edge_t, and AMOS::ScaffoldEdge_t.

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

Reimplemented in AMOS::ContigEdge_t, AMOS::Edge_t, and AMOS::ScaffoldEdge_t. Definition at line 19 of file Edge_AMOS.cc. References AMOS_THROW_ARGUMENT, clear(), AMOS::F_LINK, and AMOS::ID_t. Referenced by AMOS::ScaffoldEdge_t::readMessage(), AMOS::Edge_t::readMessage(), and AMOS::ContigEdge_t::readMessage().

void IEdge_t::readRecord (  std::istream &  fix, std::istream &  var )  [protected, virtual]

Reimplemented in AMOS::ContigEdge_t, AMOS::Edge_t, and AMOS::ScaffoldEdge_t. Definition at line 53 of file Edge_AMOS.cc. References AMOS::NULL_ID, AMOS::Pos_t, AMOS::readLE(), and AMOS::Size_t. Referenced by AMOS::ScaffoldEdge_t::readRecord(), AMOS::Edge_t::readRecord(), and AMOS::ContigEdge_t::readRecord().

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

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 AMOS::ContigEdge_t::setContigLinks(), and AMOS::ScaffoldEdge_t::setScaffoldLinks().

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

Reimplemented in AMOS::ContigEdge_t, AMOS::Edge_t, and AMOS::ScaffoldEdge_t. Definition at line 65 of file Edge_AMOS.cc. References clear(), AMOS::F_LINK, and AMOS::NULL_STRING. Referenced by AMOS::ScaffoldEdge_t::writeMessage(), AMOS::Edge_t::writeMessage(), and AMOS::ContigEdge_t::writeMessage().

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

Reimplemented in AMOS::ContigEdge_t, AMOS::Edge_t, and AMOS::ScaffoldEdge_t. Definition at line 94 of file Edge_AMOS.cc. References AMOS::Pos_t, AMOS::Size_t, and AMOS::writeLE(). Referenced by AMOS::ScaffoldEdge_t::writeRecord(), AMOS::Edge_t::writeRecord(), and AMOS::ContigEdge_t::writeRecord().

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

• Edge_AMOS.hh
• Edge_AMOS.cc

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