AMOS::Feature_t Class Reference

Notes remarkable features of other objects. More...

#include <Feature_AMOS.hh>

Inheritance diagram for AMOS::Feature_t:

[legend]Collaboration diagram for AMOS::Feature_t:

[legend]List of all members.


Public Member Functions
	Feature_t ()
	Constructs an empty Feature_t object.
	Feature_t (const Feature_t &source)
	Copy constructor.
	~Feature_t ()
	Destroys a Feature_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
Range_t	getRange () const
	Get the feature range.
std::pair< ID_t, NCode_t >	getSource () const
	Get the feature source IID and type.
FeatureType_t	getType () const
	Get the feature type.
void	setRange (Range_t range)
	Set the feature range.
void	setSource (std::pair< ID_t, NCode_t > source)
	Set the feature source IID and type.
void	setType (FeatureType_t type)
	Set the feature type.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
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_FEATURE
	The NCode type identifier for this object.
const FeatureType_t	NULL_FEATURE = 0
const FeatureType_t	REPEAT = 'R'
const FeatureType_t	UNITIG = 'U'
const FeatureType_t	JOIN = 'J'
const FeatureType_t	COVERAGE = 'C'
const FeatureType_t	ORF = 'O'
const FeatureType_t	POLYMORPHISM = 'P'
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

Notes remarkable features of other objects.

Allows a range from some other Universal object to be flagged as a feature. One example would be a location on a contig where a repeat is known to exist. Multiple repeat features with the same consensus could then be grouped together with the Group object to represent a repeat class,

Definition at line 31 of file Feature_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Feature_t::Feature_t ( ) [inline]

Constructs an empty Feature_t object.
Sets all members to zero or NULL Definition at line 70 of file Feature_AMOS.hh.
References NULL_FEATURE, AMOS::NULL_ID, and AMOS::NULL_NCODE.

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

Copy constructor.
Definition at line 81 of file Feature_AMOS.hh.

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

Destroys a Feature_t object.
Definition at line 90 of file Feature_AMOS.hh.

Member Function Documentation

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

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.
Definition at line 97 of file Feature_AMOS.hh.
References NULL_FEATURE, 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<<().

virtual NCode_t AMOS::Feature_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 107 of file Feature_AMOS.hh.
References AMOS::NCode_t.

Range_t AMOS::Feature_t::getRange ( ) const [inline]

Get the feature range.

Returns:
The feature range
Definition at line 118 of file Feature_AMOS.hh.

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

Get the feature source IID and type.
This method only returns the IID of the object which this feature refers to. The entire source object can be obtained by fetching the returned IID from the specified bank type.

Returns:
The IID of the feature source and the NCode type indentifier
Definition at line 133 of file Feature_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.

FeatureType_t AMOS::Feature_t::getType ( ) const [inline]

Get the feature type.

Returns:
The feature type
Definition at line 144 of file Feature_AMOS.hh.
References AMOS::FeatureType_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 Feature_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 29 of file Feature_AMOS.cc.
References AMOS_THROW_ARGUMENT, clear(), AMOS::Encode(), AMOS::F_CLEAR, AMOS::F_SOURCE, AMOS::F_TYPE, AMOS::NCODE_SIZE, and AMOS::Universal_t::readMessage().

void Feature_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 77 of file Feature_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::Feature_t::setRange ( Range_t range ) [inline]

Set the feature range.

Parameters:

range The new feature range

Returns:
void
Definition at line 156 of file Feature_AMOS.hh.

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

Set the feature source IID and type.

Parameters:

source The new IID and NCode type identifier of the feature source

Returns:
void
Definition at line 168 of file Feature_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 AMOS::Feature_t::setType ( FeatureType_t type ) [inline]

Set the feature type.

Parameters:

type The new feature type

Returns:
void
Definition at line 180 of file Feature_AMOS.hh.
References AMOS::FeatureType_t.

void Feature_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 90 of file Feature_AMOS.cc.
References clear(), AMOS::Decode(), AMOS::F_CLEAR, AMOS::F_SOURCE, AMOS::F_TYPE, NULL_FEATURE, AMOS::NULL_ID, AMOS::NULL_NCODE, AMOS::NULL_STRING, and AMOS::Universal_t::writeMessage().

void Feature_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 129 of file Feature_AMOS.cc.
References AMOS::writeLE(), and AMOS::Universal_t::writeRecord().

Member Data Documentation

const FeatureType_t Feature_t::COVERAGE = 'C' [static]

Definition at line 23 of file Feature_AMOS.cc.

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 FeatureType_t Feature_t::JOIN = 'J' [static]

Definition at line 22 of file Feature_AMOS.cc.

const NCode_t Feature_t::NCODE = M_FEATURE [static]

The NCode type identifier for this object.

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

const FeatureType_t Feature_t::NULL_FEATURE = 0 [static]

Definition at line 19 of file Feature_AMOS.cc.
Referenced by clear(), Feature_t(), and writeMessage().

const FeatureType_t Feature_t::ORF = 'O' [static]

Definition at line 24 of file Feature_AMOS.cc.

const FeatureType_t Feature_t::POLYMORPHISM = 'P' [static]

Definition at line 25 of file Feature_AMOS.cc.

const FeatureType_t Feature_t::REPEAT = 'R' [static]

Definition at line 20 of file Feature_AMOS.cc.

const FeatureType_t Feature_t::UNITIG = 'U' [static]

Definition at line 21 of file Feature_AMOS.cc.

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::Feature_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