AMOS::Library_t Class Reference

A collection of cloned, size-controlled DNA molecules. More...

#include <Library_AMOS.hh>

Inheritance diagram for AMOS::Library_t:

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

Public Member Functions
	Library_t ()
	Constructs an empty Library_t object.
	Library_t (const Library_t &source)
	Copy constructor.
	~Library_t ()
	Destroys a Library_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
Distribution_t	getDistribution () const
	Get the insert fragment size distribution.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setDistribution (Distribution_t dist)
	Set the insert fragment size distribution.
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_LIBRARY
	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"

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Detailed Description

A collection of cloned, size-controlled DNA molecules.

A DNA sequence library contains a group of child fragments that follow a certain sizing distribution. This object stores that size distribution. Child fragments will point back to this object as their parent library.

Definition at line 28 of file Library_AMOS.hh.

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Constructor & Destructor Documentation

AMOS::Library_t::Library_t

(

)

[inline]

Constructs an empty Library_t object.

Definition at line 57 of file Library_AMOS.hh.

AMOS::Library_t::Library_t

(

const Library_t &

source

)

[inline]

Copy constructor.

Definition at line 66 of file Library_AMOS.hh.

AMOS::Library_t::~Library_t

(

)

[inline]

Destroys a Library_t object.

Definition at line 75 of file Library_AMOS.hh.

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Member Function Documentation

virtual void AMOS::Library_t::clear

(

)

[inline, virtual]

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.

Definition at line 82 of file Library_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<<().

Distribution_t AMOS::Library_t::getDistribution

(

)

const [inline]

Get the insert fragment size distribution.

Returns:

The insert fragment size distribution

Definition at line 94 of file Library_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::Library_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 101 of file Library_AMOS.hh.

References NCODE.

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 Library_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 22 of file Library_AMOS.cc.

References clear(), AMOS::M_DISTRIBUTION, and AMOS::Universal_t::readMessage().

virtual void AMOS::Library_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::Library_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::Library_t::setDistribution

(

Distribution_t

dist

)

[inline]

Set the insert fragment size distribution.

Parameters:

dist

The new insert fragment size distribution

Returns:

void

Definition at line 117 of file Library_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 Library_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 64 of file Library_AMOS.cc.

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

virtual void AMOS::Library_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.

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Member Data Documentation

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(), AMOS::Link_t::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(), AMOS::Link_t::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 NCode_t Library_t::NCODE = M_LIBRARY [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Universal_t.

Definition at line 51 of file Library_AMOS.hh.

Referenced by AMOS::Index_t::buildReadLibrary(), getNCode(), and writeMessage().

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

• Library_AMOS.hh
• Library_AMOS.cc

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