AMOS::Overlap_t Class Reference

An overlap relation between to sequencing reads. More...

#include <Overlap_AMOS.hh>

Inheritance diagram for AMOS::Overlap_t:

[legend]Collaboration diagram for AMOS::Overlap_t:

[legend]List of all members.


Public Member Functions
	Overlap_t ()
	Constructs an empty Overlap_t object.
	Overlap_t (const Overlap_t &source)
	Copy constructor.
	~Overlap_t ()
	Destroys a Overlap_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
void	flip ()
	Flip the orientation of the overlap.
OverlapAdjacency_t	getAdjacency () const
	Get the overlapping ends of the reads.
Size_t	getAhang () const
	Get the A-hang overlap value.
Size_t	getBhang () const
	Get the B-hang overlap value.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
std::pair< ID_t, ID_t >	getReads () const
	Get the pair of contig IIDs joined by this overlap.
uint32_t	getScore () const
	Get the overlap score.
bool	isFlagC () const
	Check the value of flag C.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
void	setAdjacency (OverlapAdjacency_t adj)
	Set the overlapping ends of the reads.
void	setAhang (Size_t aHang)
	Set the A-hang overlap value.
void	setBhang (Size_t bHang)
	Set the B-hang overlap value.
void	setFlagC (bool flag)
	Set the value of flag C.
void	setReads (std::pair< ID_t, ID_t > reads)
	Set the read IID pair for this overlap.
void	setScore (uint32_t score)
	Set the overlap score.
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_OVERLAP
	The NCode type identifier for this object.
const OverlapAdjacency_t	NULL_ADJACENCY = 0
const OverlapAdjacency_t	NORMAL = 'N'
	E,B.
const OverlapAdjacency_t	ANTINORMAL = 'A'
	B,E.
const OverlapAdjacency_t	INNIE = 'I'
	E,E.
const OverlapAdjacency_t	OUTIE = 'O'
	B,B.
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"
Static Protected Attributes
const uint8_t	NORMAL_BITS = 0x1
const uint8_t	ANTINORMAL_BITS = 0x2
const uint8_t	INNIE_BITS = 0x3
const uint8_t	OUTIE_BITS = 0x0
const uint8_t	ADJACENCY_BITS = 0x3
	adjacency info mask
const uint8_t	ADJACENCY_BIT = 0x4
	adjacency exists flag
const uint8_t	FLAGC_BIT = 0x8
	C flag.

Detailed Description

An overlap relation between to sequencing reads.

A similarity based overlap between two Read_t that suggests their relative location (to one another) in the original sequence. If storing a large number of overlaps in an AMOS bank, it is wise to omit the IID and EID fields from the objects as these values will only be written to the bank if they are non-NULL. Also, an extra bit flag (FlagC) is provided in addition to FlagA and FlagB which are inherited.

Definition at line 33 of file Overlap_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Overlap_t::Overlap_t ( ) [inline]

Constructs an empty Overlap_t object.
Sets all members to 0 Definition at line 80 of file Overlap_AMOS.hh.
References AMOS::NULL_ID.

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

Copy constructor.
Definition at line 91 of file Overlap_AMOS.hh.

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

Destroys a Overlap_t object.
Definition at line 100 of file Overlap_AMOS.hh.

Member Function Documentation

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

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.
Definition at line 107 of file Overlap_AMOS.hh.
References AMOS::Universal_t::clear(), and AMOS::NULL_ID.
Referenced by readMessage(), and writeMessage().

void Overlap_t::flip ( )

Flip the orientation of the overlap.
Reverses the order of the read IIDs and changes the overlap adjacency as altered by the new orientation of the reads. Does not alter adjacency if it is currently a NULL_ADJACENCY. Also, swaps the a/bHang values. After flip, NORMAL becomes ANTINORMAL, ANTINORMAL becomes NORMAL, and INNIE and OUTIE remain the same.

Returns:
void
Definition at line 27 of file Overlap_AMOS.cc.
References ANTINORMAL, getAdjacency(), NORMAL, AMOS::OverlapAdjacency_t, setAdjacency(), and AMOS::Size_t.

OverlapAdjacency_t Overlap_t::getAdjacency ( ) const

Get the overlapping ends of the reads.
Get the overlap information for the reads, i.e. [N]ORMAL (EB), [A]NTINORMAL (BE), [I]NNIE (EE) or [O]UTIE (BB). Where B is the beginning of the read and E is the end of the read and [N]ORMAL means the end of read1 overlaps the beginning of read2.

Returns:
The pair of adjacent ends
Definition at line 44 of file Overlap_AMOS.cc.
References ADJACENCY_BIT, ADJACENCY_BITS, ANTINORMAL, ANTINORMAL_BITS, INNIE, INNIE_BITS, NORMAL, NORMAL_BITS, NULL_ADJACENCY, OUTIE, OUTIE_BITS, and AMOS::OverlapAdjacency_t.
Referenced by flip(), and writeMessage().

Size_t AMOS::Overlap_t::getAhang ( ) const [inline]

Get the A-hang overlap value.
Get the length of the non-overlapping portion of the first read.

Returns:
The A-hang overlap value
Definition at line 150 of file Overlap_AMOS.hh.
References AMOS::Size_t.

Size_t AMOS::Overlap_t::getBhang ( ) const [inline]

Get the B-hang overlap value.
Get the length of the non-overlapping portion of the second read.

Returns:
The B-hang overlap value
Definition at line 163 of file Overlap_AMOS.hh.
References AMOS::Size_t.

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<<().

virtual NCode_t AMOS::Overlap_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 170 of file Overlap_AMOS.hh.
References AMOS::NCode_t.

std::pair<ID_t, ID_t> AMOS::Overlap_t::getReads ( ) const [inline]

Get the pair of contig IIDs joined by this overlap.

Returns:
The first and second read IIDs joined by this overlap
Definition at line 181 of file Overlap_AMOS.hh.

uint32_t AMOS::Overlap_t::getScore ( ) const [inline]

Get the overlap score.

Returns:
A 32-bit unsigned integer representing the overlap score
Definition at line 192 of file Overlap_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.

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 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 writeMessage().

bool AMOS::Overlap_t::isFlagC ( ) const [inline]

Check the value of flag C.

Returns:
The value of flag C
Definition at line 203 of file Overlap_AMOS.hh.
References FLAGC_BIT.
Referenced by 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 Overlap_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 61 of file Overlap_AMOS.cc.
References AMOS_THROW_ARGUMENT, clear(), AMOS::F_ADJACENCY, AMOS::F_AHANG, AMOS::F_BHANG, AMOS::F_FLAG, AMOS::F_READS, AMOS::F_SCORE, AMOS::Universal_t::readMessage(), setAdjacency(), AMOS::IBankable_t::setFlagA(), AMOS::IBankable_t::setFlagB(), and setFlagC().

void Overlap_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 135 of file Overlap_AMOS.cc.
References AMOS::readLE(), and AMOS::Universal_t::readRecord().

void Overlap_t::setAdjacency ( OverlapAdjacency_t adj )

Set the overlapping ends of the reads.
Set the overlap information for the reads, i.e. [N]ORMAL (EB), [A]NTINORMAL (BE), [I]NNIE (EE) or [O]UTIE (BB). Where B is the beginning of the read and E is the end of the read and EB would mean the end of read1 overlaps the beginning of read2.

Note:
Will store info in nibble portion of BankFlags

Parameters:

adj The new adjacency of the reads

Precondition:
adj must be one of [NAIO]

Exceptions:

ArgumentException_t

Returns:
void
Definition at line 148 of file Overlap_AMOS.cc.
References ADJACENCY_BIT, ADJACENCY_BITS, AMOS_THROW_ARGUMENT, ANTINORMAL, ANTINORMAL_BITS, INNIE, INNIE_BITS, NORMAL, NORMAL_BITS, NULL_ADJACENCY, OUTIE, OUTIE_BITS, and AMOS::OverlapAdjacency_t.
Referenced by flip(), and readMessage().

void AMOS::Overlap_t::setAhang ( Size_t aHang ) [inline]

Set the A-hang overlap value.
Set the length of the non-overlapping portion of the first read.

Parameters:

aHang The new A-hang overlap value

Returns:
The new A-hang overlap value
Definition at line 239 of file Overlap_AMOS.hh.
References AMOS::Size_t.

void AMOS::Overlap_t::setBhang ( Size_t bHang ) [inline]

Set the B-hang overlap value.
Set the length of the non-overlapping portion of the second read.

Parameters:

bHang The new B-hang overlap value

Returns:
The new B-hang overlap value
Definition at line 253 of file Overlap_AMOS.hh.
References AMOS::Size_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 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 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 readMessage().

void AMOS::Overlap_t::setFlagC ( bool flag ) [inline]

Set the value of flag C.

Parameters:

flag The new flag C value

Returns:
void
Definition at line 265 of file Overlap_AMOS.hh.
References FLAGC_BIT.
Referenced by 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::Overlap_t::setReads ( std::pair< ID_t, ID_t > reads ) [inline]

Set the read IID pair for this overlap.

Parameters:

reads The new pair of read IIDs

Definition at line 279 of file Overlap_AMOS.hh.

void AMOS::Overlap_t::setScore ( uint32_t score ) [inline]

Set the overlap score.

Parameters:

score A 32-bit unsigned integer representing the overlap score

Returns:
void
Definition at line 291 of file Overlap_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 Overlap_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 171 of file Overlap_AMOS.cc.
References clear(), AMOS::F_ADJACENCY, AMOS::F_AHANG, AMOS::F_BHANG, AMOS::F_FLAG, AMOS::F_READS, AMOS::F_SCORE, getAdjacency(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), isFlagC(), NULL_ADJACENCY, AMOS::NULL_ID, AMOS::NULL_STRING, and AMOS::Universal_t::writeMessage().

void Overlap_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 222 of file Overlap_AMOS.cc.
References AMOS::writeLE(), and AMOS::Universal_t::writeRecord().

Member Data Documentation

const uint8_t AMOS::Overlap_t::ADJACENCY_BIT = 0x4 [static, protected]

adjacency exists flag
Definition at line 51 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().

const uint8_t AMOS::Overlap_t::ADJACENCY_BITS = 0x3 [static, protected]

adjacency info mask
Definition at line 50 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().

const OverlapAdjacency_t Overlap_t::ANTINORMAL = 'A' [static]

B,E.
Definition at line 21 of file Overlap_AMOS.cc.
Referenced by flip(), getAdjacency(), and setAdjacency().

const uint8_t AMOS::Overlap_t::ANTINORMAL_BITS = 0x2 [static, protected]

Definition at line 47 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().

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().

const uint8_t AMOS::Overlap_t::FLAGC_BIT = 0x8 [static, protected]

C flag.
Definition at line 52 of file Overlap_AMOS.hh.
Referenced by isFlagC(), and setFlagC().

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 OverlapAdjacency_t Overlap_t::INNIE = 'I' [static]

E,E.
Definition at line 22 of file Overlap_AMOS.cc.
Referenced by getAdjacency(), and setAdjacency().

const uint8_t AMOS::Overlap_t::INNIE_BITS = 0x3 [static, protected]

Definition at line 48 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().

const NCode_t Overlap_t::NCODE = M_OVERLAP [static]

The NCode type identifier for this object.

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

const OverlapAdjacency_t Overlap_t::NORMAL = 'N' [static]

E,B.
Definition at line 20 of file Overlap_AMOS.cc.
Referenced by flip(), getAdjacency(), and setAdjacency().

const uint8_t AMOS::Overlap_t::NORMAL_BITS = 0x1 [static, protected]

Definition at line 46 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().

const OverlapAdjacency_t Overlap_t::NULL_ADJACENCY = 0 [static]

Definition at line 19 of file Overlap_AMOS.cc.
Referenced by getAdjacency(), setAdjacency(), and writeMessage().

const OverlapAdjacency_t Overlap_t::OUTIE = 'O' [static]

B,B.
Definition at line 23 of file Overlap_AMOS.cc.
Referenced by getAdjacency(), and setAdjacency().

const uint8_t AMOS::Overlap_t::OUTIE_BITS = 0x0 [static, protected]

Definition at line 49 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().

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

Generated on Tue May 17 15:19:49 2005 for libAMOS by

1.3.8

AMOS::Overlap_t Class Reference

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation