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AMOS::Read_t Class Reference

A DNA sequencing read. More...

#include <Read_AMOS.hh>

Inheritance diagram for AMOS::Read_t:

[legend]Collaboration diagram for AMOS::Read_t:

[legend]List of all members.

Public Methods
	Read_t ()
	Constructs an empty Read_t object.
	Read_t (const Read_t &source)
	Copy constructor.
	~Read_t ()
	Destroys a Read_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
Range_t	getClearRange ()
	Get the generic clear range.
ID_t	getFragment () const
	Get the parent fragment ID.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
Range_t	getQualityClearRange ()
	Get the quality score clear range.
ReadType_t	getType () const
	Get the type of read.
Range_t	getVectorClearRange ()
	Get the vector sequence clear range.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setClearRange (Range_t clear)
	Set the generic clear range.
void	setFragment (ID_t frag)
	Set the parent fragment ID.
void	setQualityClearRange (Range_t qclear)
	Set the quality score clear range.
void	setType (ReadType_t type)
	Set the type of read.
void	setVectorClearRange (Range_t vclear)
	Set the vector sequence clear range.
virtual void	writeMessage (Message_t &msg) const
	Writes data to a Message object.
Static Public Methods
NCode_t	NCode ()
	Get the AMOS NCode type identifier (statically).
Static Public Attributes
const ReadType_t	NULL_READ = 0
const ReadType_t	OTHER = 'X'
const ReadType_t	END = 'E'
const ReadType_t	CONTIG = 'C'
const ReadType_t	BAC = 'B'
const ReadType_t	WALK = 'W'
Protected Methods
virtual void	readRecord (std::istream &fix, std::istream &var)
	Read selected class members from a biserial record.
virtual Size_t	sizeVar () const
	Returns the current size of the variable length record.
virtual void	writeRecord (std::ostream &fix, std::ostream &var) const
	Write selected class members to a biserial record.

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Detailed Description

A DNA sequencing read.

Derived from a Sequence_t type, this class is for the efficient storage of DNA sequencing reads. Retains all the functionality of a Sequence with added fields for clear ranges, mate pairs, etc.

Todo:

add more clear range flexibility

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Constructor & Destructor Documentation

AMOS::Read_t::Read_t (    )  [inline]

Constructs an empty Read_t object. Sets all members to NULL

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

Copy constructor.

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

Destroys a Read_t object.

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Member Function Documentation

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

Clears all object data, reinitializes the object. All data will be cleared, but object compression status will remain unchanged. Use the compress/uncompress members to change this info. Reimplemented from AMOS::Sequence_t.

Range_t AMOS::Read_t::getClearRange (    )  [inline]

Get the generic clear range. Returns: The generic clear range

ID_t AMOS::Read_t::getFragment (    )  const [inline]

Get the parent fragment ID. Returns: The parent fragment ID

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

Get the AMOS NCode type identifier. Returns: The AMOS NCode type identifier Reimplemented from AMOS::Sequence_t.

Range_t AMOS::Read_t::getQualityClearRange (    )  [inline]

Get the quality score clear range. Returns: The quality score clear range

ReadType_t AMOS::Read_t::getType (    )  const [inline]

Get the type of read. Returns: The type of read

Range_t AMOS::Read_t::getVectorClearRange (    )  [inline]

Get the vector sequence clear range. Returns: The vector sequence clear range

NCode_t AMOS::Read_t::NCode (    )  [inline, static]

Get the AMOS NCode type identifier (statically). Can be used for constructing a Bank with a certain NCode. e.g. 'Bank_t (Read_t::NCode( ))' Returns: The AMOS NCode type identifier Reimplemented from AMOS::Sequence_t.

void Read_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::Sequence_t.

void Read_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::Sequence_t.

void AMOS::Read_t::setClearRange (  Range_t    clear )  [inline]

Set the generic clear range. Parameters: clear  The new generic clear range Returns: void

void AMOS::Read_t::setFragment (  ID_t    frag )  [inline]

Set the parent fragment ID. Parameters: frag  The new parent fragment ID Returns: void

void AMOS::Read_t::setQualityClearRange (  Range_t    qclear )  [inline]

Set the quality score clear range. Parameters: qclear  The new quality score clear range Returns: void

void AMOS::Read_t::setType (  ReadType_t    type )  [inline]

Set the type of read. Parameters: type  The new type of read Precondition: type is one of [XECBW] Exceptions: ArgumentException_t  Returns: void

void AMOS::Read_t::setVectorClearRange (  Range_t    vclear )  [inline]

Set the vector sequence clear range. Parameters: vclear  The new vector sequence clear range Returns: void

Size_t Read_t::sizeVar (    )  const [protected, virtual]

Returns the current size of the variable length record. Returns: Size of the variable length record (var stream) Reimplemented from AMOS::Sequence_t.

void Read_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::Sequence_t.

void Read_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. Will only write to the ready streams, but the size of the record will always be returned. Does not write the flags and 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::Sequence_t.

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Member Data Documentation

const ReadType_t AMOS::Read_t::BAC = 'B' [static]

const ReadType_t AMOS::Read_t::CONTIG = 'C' [static]

const ReadType_t AMOS::Read_t::END = 'E' [static]

const ReadType_t AMOS::Read_t::NULL_READ = 0 [static]

const ReadType_t AMOS::Read_t::OTHER = 'X' [static]

const ReadType_t AMOS::Read_t::WALK = 'W' [static]

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

• Read_AMOS.hh
• Read_AMOS.cc

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