AMOS::Tile_t

AMOS::Tile_t Struct Reference

A singe sequence's location and orientation in a larger sequence. More...

#include <datatypes_AMOS.hh>

Inheritance diagram for AMOS::Tile_t:

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


Public Member Functions
	Tile_t ()
	Constructs an empty Tile_t object.
	~Tile_t ()
	Destroys a Tile_t object.
void	clear ()
	Clears all object data, reinitializes the object.
Size_t	getGappedLength () const
	Gets the gapped length of the tile.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
Pos_t	getRightOffset () const
	Gets the exact right offset of the tile.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	readRecord (std::istream &in)
	Read a binary record.
virtual void	writeMessage (Message_t &msg) const
	Writes data to a Message object.
void	writeRecord (std::ostream &out) const
	Write a binary record.
Public Attributes
ID_t	source
	the source of the tile, e.g. read IID
std::vector< Pos_t >	gaps
	the absolute gap positions
Pos_t	offset
	the offset of the tile
Range_t	range
	the usable range of the tile
Static Public Attributes
static const NCode_t	NCODE = M_TILE
	The NCode type identifier for this object.

Detailed Description

A singe sequence's location and orientation in a larger sequence.

A tiled sequence, like a read in a contig, or a contig in a scaffold. For explanation purposes, let us assume we are dealing with an underlying read in a contig. The id is the IID of the read. The gaps are the alignment gaps in the read, stored as a list of gap positions. How these positions are stored relative to the parent contig is left to the user. Commonly, each gap integer is simply the gap location in the read. Thus, two adjacent gaps would share the same value. The offset is the offset of the beginning on the read in the contig, thus an offset of 0 would signify a read beginning at the very start of the contig. Finally, the range is the portion of the read that has been aligned to the contig, with the range order also specifying the orientation of the read relative to the contig, i.e. if the beginning of the range is greater than the end of the range the read is reversed relative to the forward strand of the contig.

Definition at line 301 of file datatypes_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Tile_t::Tile_t ( ) [inline]

Constructs an empty Tile_t object.

Sets id to NULL_ID, offset to 0

Definition at line 318 of file datatypes_AMOS.hh.

References AMOS::NULL_ID, offset, and source.

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

Destroys a Tile_t object.

Definition at line 328 of file datatypes_AMOS.hh.

Member Function Documentation

void Tile_t::clear ( )

Clears all object data, reinitializes the object.

Definition at line 99 of file datatypes_AMOS.cc.

References gaps, AMOS::NULL_ID, offset, range, and source.

Referenced by readMessage(), and writeMessage().

Size_t AMOS::Tile_t::getGappedLength ( ) const [inline]

Gets the gapped length of the tile.

(range . getLength( ) + gaps . size( ))

Returns:: The gapped length of the tile

Definition at line 347 of file datatypes_AMOS.hh.

References gaps, and range.

Referenced by AMOS::TileOrderCmp::operator()(), and AMOS::TiledRead_t::TiledRead_t().

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

Get the AMOS NCode type identifier.

Returns:: The AMOS NCode type identifier

Implements AMOS::IMessagable_t.

Definition at line 354 of file datatypes_AMOS.hh.

References NCODE.

Referenced by writeMessage().

Pos_t AMOS::Tile_t::getRightOffset ( ) const [inline]

Gets the exact right offset of the tile.

offset + (range . getLength( ) + gaps . size( )) - 1

Returns:: The right offset of the tile

Definition at line 368 of file datatypes_AMOS.hh.

References gaps, AMOS::Range_t::getLength(), offset, and range.

void Tile_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