AMOS::Scaffold_t Class Reference

A ordered, oriented and positioned list of contigs. More...

#include <Scaffold_AMOS.hh>

Inheritance diagram for AMOS::Scaffold_t:

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


Public Member Functions
	Scaffold_t ()
	Constructs an empty Scaffold_t object.
	Scaffold_t (const Scaffold_t &source)
	Copy constructor.
	~Scaffold_t ()
	Destroys a Scaffold_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
const std::vector< Tile_t > &	getContigTiling () const
	Get the tiling of underlying contigs.
std::vector< Tile_t > &	getContigTiling ()
	Get the tiling of underlying contigs.
const std::vector< ID_t > &	getContigEdges () const
	Get the contig edge IIDs.
std::vector< ID_t > &	getContigEdges ()
	Get the contig edge IIDs.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
Size_t	getSpan () const
	Get the span of the contig layout.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setContigTiling (const std::vector< Tile_t > &contigs)
	Set the tiling of underlying contigs.
void	setContigTiling (const Layout_t &layout)
	Set the tiling of underlying contigs.
void	setContigEdges (const std::vector< ID_t > &edges)
	Set the contig edge IIDs.
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_SCAFFOLD
	The NCode type identifier for this object.
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"

Detailed Description

A ordered, oriented and positioned list of contigs.

A list of contigs that are ordered, oriented and positioned in relation to one another.

Definition at line 29 of file Scaffold_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Scaffold_t::Scaffold_t ( ) [inline]

Constructs an empty Scaffold_t object.

Definition at line 61 of file Scaffold_AMOS.hh.

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

Copy constructor.

Definition at line 70 of file Scaffold_AMOS.hh.

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

Destroys a Scaffold_t object.

Definition at line 79 of file Scaffold_AMOS.hh.

Member Function Documentation

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

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.

Definition at line 86 of file Scaffold_AMOS.hh.

References AMOS::Universal_t::clear().

Referenced by readMessage(), 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<<().

std::vector<ID_t>& AMOS::Scaffold_t::getContigEdges ( ) [inline]

Get the contig edge IIDs.

Returns:: The vector of contig edge IIDs

Definition at line 132 of file Scaffold_AMOS.hh.

const std::vector<ID_t>& AMOS::Scaffold_t::getContigEdges ( ) const [inline]

Get the contig edge IIDs.

Returns:: The vector of contig edge IIDs

Definition at line 121 of file Scaffold_AMOS.hh.

std::vector<Tile_t>& AMOS::Scaffold_t::getContigTiling ( ) [inline]

Get the tiling of underlying contigs.

Returns:: The vector of underlying contigs

Definition at line 110 of file Scaffold_AMOS.hh.

const std::vector<Tile_t>& AMOS::Scaffold_t::getContigTiling ( ) const [inline]

Get the tiling of underlying contigs.

Returns:: The vector of underlying contigs

Definition at line 99 of file Scaffold_AMOS.hh.

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

Get the AMOS NCode type identifier.

Returns:: The AMOS NCode type identifier

Reimplemented from AMOS::Universal_t.

Definition at line 139 of file Scaffold_AMOS.hh.

References NCODE.

Size_t Scaffold_t::getSpan ( ) const

Get the span of the contig layout.

Returns the difference between min(offset) and max(offset+len). Since the layout is not necessarily sorted, this method requires linear time.

Returns:: The span of the layout

Definition at line 22 of file Scaffold_AMOS.cc.

References AMOS::MAX_POS.

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.

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 Scaffold_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.

Definition at line 51 of file Scaffold_AMOS.cc.

References AMOS_THROW_ARGUMENT, clear(), AMOS::F_EDGE, AMOS::M_TILE, and AMOS::Universal_t::readMessage().

virtual void AMOS::Scaffold_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.

virtual void AMOS::Scaffold_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.

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::Scaffold_t::setContigEdges ( const std::vector< ID_t > & edges ) [inline]

Set the contig edge IIDs.

Parameters:

edges

The new vector of contig edge IIDs

Returns:: void

Definition at line 190 of file Scaffold_AMOS.hh.

void AMOS::Scaffold_t::setContigTiling ( const Layout_t & layout ) [inline]

Set the tiling of underlying contigs.

Parameters:

layout

The new contig layout

Returns:: void

Definition at line 178 of file Scaffold_AMOS.hh.

void AMOS::Scaffold_t::setContigTiling ( const std::vector< Tile_t > & contigs ) [inline]

Set the tiling of underlying contigs.

Parameters:

contigs

The new vector of underlying contigs

Returns:: void

Definition at line 166 of file Scaffold_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::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 Scaffold_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.

Definition at line 132 of file Scaffold_AMOS.cc.

References clear(), AMOS::F_EDGE, NCODE, AMOS::NULL_STRING, and AMOS::Universal_t::writeMessage().

virtual void AMOS::Scaffold_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.