AMOS::Fragment_t Class Reference

Single piece of DNA. More...

#include <Fragment_AMOS.hh>

Inheritance diagram for AMOS::Fragment_t:

[legend]Collaboration diagram for AMOS::Fragment_t:

[legend]List of all members.


Public Member Functions
	Fragment_t ()
	Contstructs an empty Fragment_t object.
	Fragment_t (const Fragment_t &source)
	Copy constructor.
	~Fragment_t ()
	Destroys a Fragment_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
ID_t	getLibrary () const
	Get the parent library IID.
std::pair< ID_t, ID_t >	getMatePair () const
	Get the paired sequencing reads for this fragment.
Size_t	getSize () const
	Get the size of the fragment, if known.
std::pair< ID_t, NCode_t >	getSource () const
	Get the fragment source IID and type.
FragmentType_t	getType () const
	Get the fragment type.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setLibrary (ID_t library)
	Set the parent library IID.
void	setReads (std::pair< ID_t, ID_t > reads)
	Set the paired sequencing reads for this fragment.
void	setSize (Size_t size)
	Set the size of the fragment, if known.
void	setSource (std::pair< ID_t, NCode_t > source)
	Set the link source IID and type.
void	setType (FragmentType_t type)
	Set the fragment type.
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
const NCode_t	NCODE = M_FRAGMENT
	The NCode type identifier for this object.
const FragmentType_t	NULL_FRAGMENT = 0
const FragmentType_t	OTHER = 'X'
const FragmentType_t	BAC = 'B'
const FragmentType_t	INSERT = 'I'
const FragmentType_t	TRANSPOSON = 'T'
const FragmentType_t	WALK = 'W'
Protected Member Functions
virtual void	readRecord (std::istream &fix, std::istream &var)
	Read selected class members from a biserial record.
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

Single piece of DNA.

A single piece of DNA from which a group of reads were sequenced. This allows for the hierarchical clustering of reads that come from the same fragment. Mate-pair information is also stored in this type.

Definition at line 30 of file Fragment_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Fragment_t::Fragment_t ( ) [inline]

Contstructs an empty Fragment_t object.
Sets all members to NULL Definition at line 70 of file Fragment_AMOS.hh.
References NULL_FRAGMENT, AMOS::NULL_ID, and AMOS::NULL_NCODE.

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

Copy constructor.
Definition at line 82 of file Fragment_AMOS.hh.

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

Destroys a Fragment_t object.
Definition at line 91 of file Fragment_AMOS.hh.

Member Function Documentation

void Fragment_t::clear ( ) [virtual]

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.
Definition at line 28 of file Fragment_AMOS.cc.
References AMOS::Universal_t::clear(), NULL_FRAGMENT, AMOS::NULL_ID, and AMOS::NULL_NCODE.
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 110 of file Universal_AMOS.hh.
Referenced by AMOS::operator<<().

const std::string& AMOS::IBankable_t::getEID ( ) const [inline, inherited]

Get the external ID.

Returns:
The external ID
Definition at line 156 of file Bank_AMOS.hh.
References AMOS::IBankable_t::eid_m.
Referenced by AMOS::Contig_t::writeUMD().

ID_t AMOS::IBankable_t::getIID ( ) const [inline, inherited]

Get the internal ID.

Returns:
The internal ID
Definition at line 167 of file Bank_AMOS.hh.
References AMOS::ID_t, and 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<<().

ID_t AMOS::Fragment_t::getLibrary ( ) const [inline]

Get the parent library IID.

Returns:
The IID of the parent library
Definition at line 113 of file Fragment_AMOS.hh.
References AMOS::ID_t.

std::pair<ID_t, ID_t> AMOS::Fragment_t::getMatePair ( ) const [inline]

Get the paired sequencing reads for this fragment.
Orientation of the pair can be deduced from the fragment type. An INSERT fragment will have innie mates and a TRANSPOSON fragment will have outie mates.

Returns:
The mated reads
Definition at line 128 of file Fragment_AMOS.hh.

virtual NCode_t AMOS::Fragment_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 102 of file Fragment_AMOS.hh.
References AMOS::NCode_t.

Size_t AMOS::Fragment_t::getSize ( ) const [inline]

Get the size of the fragment, if known.
Size will be 0 if unknown. If exact size is unknown, the parent library of this fragment should contain an estimated size distribution.

Returns:
The size of the fragment
Definition at line 142 of file Fragment_AMOS.hh.
References AMOS::Size_t.

std::pair<ID_t, NCode_t> AMOS::Fragment_t::getSource ( ) const [inline]

Get the fragment source IID and type.
Returns the source this fragment was generated from, e.g. the insert fragment used for a PCR walk.

Returns:
The IID of the fragment source and the NCode type identifier
Definition at line 156 of file Fragment_AMOS.hh.

const Status_t AMOS::Universal_t::getStatus ( ) const [inline, inherited]

Get the status value.

Returns:
The status value
Definition at line 121 of file Universal_AMOS.hh.
References AMOS::Status_t.

FragmentType_t AMOS::Fragment_t::getType ( ) const [inline]

Get the fragment type.

Returns:
The type of fragment
Definition at line 167 of file Fragment_AMOS.hh.
References AMOS::FragmentType_t.

bool AMOS::IBankable_t::isFlagA ( ) const [inline, inherited]

Check the value of flag A.

Returns:
The value of flag A
Definition at line 210 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 221 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 199 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 188 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.

void Fragment_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 39 of file Fragment_AMOS.cc.
References AMOS_THROW_ARGUMENT, clear(), AMOS::Encode(), AMOS::F_LIBRARY, AMOS::F_READS, AMOS::F_SIZE, AMOS::F_SOURCE, AMOS::F_TYPE, AMOS::NCODE_SIZE, AMOS::Universal_t::readMessage(), and setType().

void Fragment_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.
Definition at line 105 of file Fragment_AMOS.cc.
References AMOS::readLE(), and AMOS::Universal_t::readRecord().

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 144 of file Universal_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 234 of file Bank_AMOS.hh.
References AMOS::IBankable_t::eid_m, and AMOS::NL_CHAR.
Referenced by AMOS::Contig_t::readUMD().

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 254 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 270 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 282 of file Bank_AMOS.hh.
References AMOS::ID_t, and AMOS::IBankable_t::iid_m.

void AMOS::Fragment_t::setLibrary ( ID_t library ) [inline]

Set the parent library IID.

Parameters:

library The new IID of parent library

Returns:
void
Definition at line 183 of file Fragment_AMOS.hh.
References AMOS::ID_t.

void AMOS::Fragment_t::setReads ( std::pair< ID_t, ID_t > reads ) [inline]

Set the paired sequencing reads for this fragment.
Orientation of the pair can be stored in the fragment type. An INSERT fragment will have innie mates and a TRANSPOSON fragment will have outie mates.

Parameters:

reads The new pair of read IIDs

Returns:
void
Definition at line 199 of file Fragment_AMOS.hh.

void AMOS::Fragment_t::setSize ( Size_t size ) [inline]

Set the size of the fragment, if known.

Parameters:

size The size of the fragment

Returns:
void
Definition at line 211 of file Fragment_AMOS.hh.
References AMOS::Size_t.

void AMOS::Fragment_t::setSource ( std::pair< ID_t, NCode_t > source ) [inline]

Set the link source IID and type.
Sets the source this fragment was generated from, e.g. the insert fragment used for a PCR walk.

Parameters:

source The IID and NCode type of the fragment source

Returns:
void
Definition at line 226 of file Fragment_AMOS.hh.

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 156 of file Universal_AMOS.hh.
References AMOS::Status_t.
Referenced by AMOS::Universal_t::readMessage().

void Fragment_t::setType ( FragmentType_t type )

Set the fragment type.

Parameters:

type The new fragment type

Precondition:
type is one of [OITB] or NULL

Exceptions:

ArgumentException_t

Returns:
void
Definition at line 120 of file Fragment_AMOS.cc.
References AMOS_THROW_ARGUMENT, BAC, AMOS::FragmentType_t, INSERT, NULL_FRAGMENT, OTHER, TRANSPOSON, and WALK.
Referenced by readMessage().

void Fragment_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 139 of file Fragment_AMOS.cc.
References clear(), AMOS::Decode(), AMOS::F_LIBRARY, AMOS::F_READS, AMOS::F_SIZE, AMOS::F_SOURCE, AMOS::F_TYPE, NULL_FRAGMENT, AMOS::NULL_ID, AMOS::NULL_NCODE, AMOS::NULL_STRING, and AMOS::Universal_t::writeMessage().

void Fragment_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.
Definition at line 192 of file Fragment_AMOS.cc.
References AMOS::writeLE(), and AMOS::Universal_t::writeRecord().

Member Data Documentation

const FragmentType_t Fragment_t::BAC = 'B' [static]

Definition at line 21 of file Fragment_AMOS.cc.
Referenced by setType().

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::IBankable_t::clear(), AMOS::IBankable_t::getEID(), and AMOS::IBankable_t::setEID().

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::IBankable_t::clear(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), AMOS::IBankable_t::isModified(), AMOS::IBankable_t::isRemoved(), AMOS::IBankable_t::setFlagA(), and AMOS::IBankable_t::setFlagB().

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::IBankable_t::clear(), AMOS::IBankable_t::getIID(), AMOS::IBankable_t::IBankable_t(), and AMOS::IBankable_t::setIID().

const FragmentType_t Fragment_t::INSERT = 'I' [static]

Definition at line 22 of file Fragment_AMOS.cc.
Referenced by setType().

const NCode_t Fragment_t::NCODE = M_FRAGMENT [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Universal_t.
Definition at line 18 of file Fragment_AMOS.cc.

const FragmentType_t Fragment_t::NULL_FRAGMENT = 0 [static]

Definition at line 19 of file Fragment_AMOS.cc.
Referenced by clear(), Fragment_t(), setType(), and writeMessage().

const FragmentType_t Fragment_t::OTHER = 'X' [static]

Definition at line 20 of file Fragment_AMOS.cc.
Referenced by setType().

const FragmentType_t Fragment_t::TRANSPOSON = 'T' [static]

Definition at line 23 of file Fragment_AMOS.cc.
Referenced by setType().

const FragmentType_t Fragment_t::WALK = 'W' [static]

Definition at line 24 of file Fragment_AMOS.cc.
Referenced by setType().

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

Generated on Tue May 17 15:19:46 2005 for libAMOS by

1.3.8

AMOS::Fragment_t Class Reference

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation