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gnBaseFeature Class Reference

Features of DNA sequences can be accessed and manipulated using classes derived from gnBaseFeature. More...

#include <gnBaseFeature.h>

Inheritance diagram for gnBaseFeature:


Public Member Functions
	gnBaseFeature ()
	gnBaseFeature (string &name, uint32 id=0, gnFragmentSpec *spec=NULL, gnLocation::gnLocationType lt=gnLocation::LT_Nothing, boolean broken=false)
	~gnBaseFeature ()
	Destructor, frees memory.
virtual gnBaseFeature *	Clone () const=0
virtual string	GetName () const
	Gets the feature name (e.g.
virtual void	SetName (const string &name)
	Sets the feature name.
virtual uint32	GetID () const
	Gets this feature's ID.
virtual void	SetID (uint32 id)
	Sets this feature's ID.
virtual gnFragmentSpec *	GetSpec () const
	Gets the gnFragmentSpec to which this feature refers.
virtual void	SetSpec (gnFragmentSpec *spec)
	Sets the gnFragmentSpec to which this feature refers.
virtual gnLocation::gnLocationType	GetLocationType () const
	Gets this feature's location type.
virtual void	SetLocationType (gnLocation::gnLocationType lType)
	Sets this feature's location type.
virtual uint32	GetLocationListLength () const
	Returns the number of locations this feature describes.
virtual boolean	AddLocation (const gnLocation &l, uint32 listI=0)
	Adds a new location before the location at listI.
virtual gnLocation	GetLocation (uint32 listI) const
	Gets the location at listI.
virtual boolean	RemoveLocation (uint32 listI)
	Deletes the location at listI.
virtual boolean	SetLocation (const gnLocation &l, uint32 listI)
	Sets the location at listI to a new location.
virtual boolean	MovePositive (const gnSeqI i)
	Increases this feature's coordinates by a specific number of bases.
virtual boolean	MoveNegative (const gnSeqI i)
	Decreases this feature's coordinates by a specific number of bases.
virtual boolean	CropStart (const gnSeqI i)
	Crops the start locations of this feature by the specified amount.
virtual boolean	CropEnd (const gnSeqI i)
	Crops the end locations of this feature by the specified amount.
virtual boolean	Crop (const gnLocation &l)
	Crops the locations of this feature to fit within the given location.
virtual boolean	IsBroken () const
	Returns true if the feature is broken.
virtual void	SetBroken (boolean broke)
	Sets whether the feature is broken or not.
virtual boolean	Contains (gnSeqI i) const
	Checks if the given coordinate is contained by this feature.
virtual boolean	Contains (const gnLocation &l) const
	Checks if the given location is contained by this feature.
virtual boolean	Contains (gnBaseFeature *feature) const
	Checks if the given feature is entirely contained by this feature.
virtual boolean	IsContainedBy (const gnLocation &l) const
	Checks if this feature is entirely contained by the given location.
virtual boolean	Intersects (const gnLocation &l) const
	Checks if the given location intersects this feature.
virtual boolean	Intersects (gnBaseFeature *feature) const
	Checks if the given feature intersects this feature.
virtual uint32	GetQualifierListLength () const
	Returns the number of qualifiers in this feature.
virtual boolean	AddQualifier (gnBaseQualifier *qualifier)
	Adds a new qualifier.
virtual boolean	HasQualifier (const string &name) const
	Looks for a qualifier by name.
virtual uint32	FirstIndexOfQualifier (const string &name, uint32 listI) const
	Searches for a qualifier by name, starting at the index listI.
virtual uint32	LastIndexOfQualifier (const string &name, uint32 listI) const
	Searches for a qualifier by name, ending at the index listI.
virtual string	GetQualifierName (uint32 listI) const
	Gets the name of the qualifier at the list index listI.
virtual string	GetQualifierValue (uint32 listI) const
	Gets the value of the qualifier at the list index listI.
virtual gnBaseQualifier *	GetQualifier (uint32 listI)
	Gets the qualifier at the list index listI.
virtual boolean	RemoveQualifier (uint32 listI)
	Deletes the qualifier at the list index listI.
virtual boolean	SetQualifier (string &name, string &value, uint32 listI)
	Set the name and value of the qualifier at the list index listI.
virtual boolean	SetQualifierName (string &name, uint32 listI)
	Set the name of the qualifier at the list index listI.
virtual boolean	SetQualifierValue (string &value, uint32 listI)
	Set the value of the qualifier at the list index listI.
Protected Attributes
uint32	m_id
string	m_name
boolean	m_broken
gnLocation::gnLocationType	m_locationType
vector< gnLocation >	m_locationList
vector< gnBaseQualifier * >	m_qualifierList
gnFragmentSpec *	m_spec

Detailed Description

Features of DNA sequences can be accessed and manipulated using classes derived from gnBaseFeature.

gnBaseFeature outlines a basic interface and gives functionality its derived sequence classes, such as gnCDSFeature.

Definition at line 30 of file gnBaseFeature.h.

Constructor & Destructor Documentation

gnBaseFeature::gnBaseFeature ( )

Definition at line 18 of file gnBaseFeature.cpp.
References gnLocation::LT_Nothing, m_broken, m_id, m_locationType, m_name, and m_spec.

gnBaseFeature::gnBaseFeature ( string & name,

uint32 id = 0,

gnFragmentSpec * spec = NULL,

gnLocation::gnLocationType lt = gnLocation::LT_Nothing,

boolean broken = false

)

Definition at line 26 of file gnBaseFeature.cpp.
References m_broken, m_id, m_locationType, m_name, and m_spec.

gnBaseFeature::~gnBaseFeature ( )

Destructor, frees memory.

Definition at line 34 of file gnBaseFeature.cpp.
References m_qualifierList, and uint32.

Member Function Documentation

boolean gnBaseFeature::AddLocation ( const gnLocation & l,

uint32 listI = 0

) [inline, virtual]

Adds a new location before the location at listI.

Parameters:

l The gnLocation to add.

listI The index into the location list to insert before.

Returns:
True if successful, false otherwise.

See also:
gnLocation

Definition at line 186 of file gnBaseFeature.cpp.
References m_locationList.
Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

boolean gnBaseFeature::AddQualifier ( gnBaseQualifier * qualifier ) [virtual]

Adds a new qualifier.

Parameters:

qualifier The qualifier to add.

Returns:
True if successful, false otherwise.

Definition at line 216 of file gnBaseFeature.cpp.
References m_qualifierList.
Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

virtual gnBaseFeature* gnBaseFeature::Clone ( ) const [pure virtual]

Implements gnClone.
Implemented in gnFeature.

boolean gnBaseFeature::Contains ( gnBaseFeature * feature ) const [virtual]

Checks if the given feature is entirely contained by this feature.

Parameters:

feature The feature to check

Returns:
True if "feature" is contained by this feature. False otherwise

Definition at line 146 of file gnBaseFeature.cpp.
References GetLocation(), GetLocationListLength(), m_locationList, and uint32.

boolean gnBaseFeature::Contains ( const gnLocation & l ) const [virtual]

Checks if the given location is contained by this feature.

Parameters:

l The location to check

Returns:
True if "l" is contained by this feature. False otherwise

Definition at line 139 of file gnBaseFeature.cpp.
References m_locationList, and uint32.

boolean gnBaseFeature::Contains ( gnSeqI i ) const [virtual]

Checks if the given coordinate is contained by this feature.

Parameters:

i The coordinate to check

Returns:
True if "i" is contained by this feature. False otherwise

Definition at line 131 of file gnBaseFeature.cpp.
References m_locationList, and uint32.

boolean gnBaseFeature::Crop ( const gnLocation & l ) [inline, virtual]

Crops the locations of this feature to fit within the given location.

Parameters:

l The location to crop reduce to.

Returns:
True if successful, false if the feature was broken by the change.

Definition at line 328 of file gnBaseFeature.h.
References CropEnd(), CropStart(), gnLocation::GetEnd(), and gnLocation::GetStart().

boolean gnBaseFeature::CropEnd ( const gnSeqI i ) [virtual]

Crops the end locations of this feature by the specified amount.

Parameters:

i The amount to crop.

Returns:
True if successful, false if the feature was broken by the change.

Definition at line 58 of file gnBaseFeature.cpp.
References m_locationList, and uint32.
Referenced by Crop().

boolean gnBaseFeature::CropStart ( const gnSeqI i ) [virtual]

Crops the start locations of this feature by the specified amount.

Parameters:

i The amount to crop.

Returns:
True if successful, false if the feature was broken by the change.

Definition at line 67 of file gnBaseFeature.cpp.
References m_locationList, and uint32.
Referenced by Crop().

uint32 gnBaseFeature::FirstIndexOfQualifier ( const string & name,

uint32 listI

) const [virtual]

Searches for a qualifier by name, starting at the index listI.

Parameters:

name The name of the qualifier to look for.

listI The index into the qualifier list to start the search at.

Returns:
The index of the qualifier.

Definition at line 74 of file gnBaseFeature.cpp.
References GNSEQI_END, m_qualifierList, and uint32.

uint32 gnBaseFeature::GetID ( ) const [inline, virtual]

Gets this feature's ID.

Returns:
The feature's ID.

Definition at line 291 of file gnBaseFeature.h.
References m_id, and uint32.

gnLocation gnBaseFeature::GetLocation ( uint32 listI ) const [virtual]

Gets the location at listI.

Parameters:

listI The index into the location list to get.

Returns:
The location.

Definition at line 194 of file gnBaseFeature.cpp.
References m_locationList.
Referenced by Contains(), Intersects(), and gnGBKSource::Write().

uint32 gnBaseFeature::GetLocationListLength ( ) const [inline, virtual]

Returns the number of locations this feature describes.

Returns:
The number of locations this feature describes.

Definition at line 324 of file gnBaseFeature.h.
References m_locationList, and uint32.
Referenced by Contains(), Intersects(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), and gnGBKSource::Write().

gnLocation::gnLocationType gnBaseFeature::GetLocationType ( ) const [inline, virtual]

Gets this feature's location type.

Returns:
The feature's location type.

See also:
gnLocationType

Definition at line 316 of file gnBaseFeature.h.
References gnLocation::gnLocationType, and m_locationType.
Referenced by gnGBKSource::Write().

string gnBaseFeature::GetName ( ) const [inline, virtual]

Gets the feature name (e.g.
CDS, trna...).
Returns:
The feature name.

Definition at line 283 of file gnBaseFeature.h.
References m_name.
Referenced by SetQualifierValue(), and gnGBKSource::Write().

gnBaseQualifier * gnBaseFeature::GetQualifier ( uint32 listI ) [virtual]

Gets the qualifier at the list index listI.

Parameters:

listI The index into the qualifier list.

Returns:
The qualifier.

Definition at line 243 of file gnBaseFeature.cpp.
References m_qualifierList.
Referenced by gnGBKSource::Write().

uint32 gnBaseFeature::GetQualifierListLength ( ) const [inline, virtual]

Returns the number of qualifiers in this feature.

Returns:
The number of qualifiers in this feature.

Definition at line 332 of file gnBaseFeature.h.
References m_qualifierList, and uint32.
Referenced by gnGBKSource::Write().

string gnBaseFeature::GetQualifierName ( uint32 listI ) const [virtual]

Gets the name of the qualifier at the list index listI.

Parameters:

listI The index into the qualifier list.

Returns:
The name of the qualifier.

Definition at line 231 of file gnBaseFeature.cpp.
References m_qualifierList.

string gnBaseFeature::GetQualifierValue ( uint32 listI ) const [virtual]

Gets the value of the qualifier at the list index listI.

Parameters:

listI The index into the qualifier list.

Returns:
The value of the qualifier.

Definition at line 237 of file gnBaseFeature.cpp.
References m_qualifierList.

gnFragmentSpec * gnBaseFeature::GetSpec ( ) const [inline, virtual]

Gets the gnFragmentSpec to which this feature refers.

Returns:
The feature's ID.

See also:
gnFragmentSpec

Definition at line 299 of file gnBaseFeature.h.
References m_spec.

boolean gnBaseFeature::HasQualifier ( const string & name ) const [virtual]

Looks for a qualifier by name.

Parameters:

name The name of the qualifier to look for.

Returns:
True if a qualifier was found, false otherwise.

Definition at line 224 of file gnBaseFeature.cpp.
References m_qualifierList, and uint32.

boolean gnBaseFeature::Intersects ( gnBaseFeature * feature ) const [virtual]

Checks if the given feature intersects this feature.

Parameters:

feature The location to check

Returns:
True if "feature" intersects this feature. False otherwise

Definition at line 173 of file gnBaseFeature.cpp.
References GetLocation(), GetLocationListLength(), m_locationList, and uint32.

boolean gnBaseFeature::Intersects ( const gnLocation & l ) const [virtual]

Checks if the given location intersects this feature.

Parameters:

l The location to check

Returns:
True if "l" intersects this feature. False otherwise

Definition at line 166 of file gnBaseFeature.cpp.
References gnLocation::Intersects(), m_locationList, and uint32.

boolean gnBaseFeature::IsBroken ( ) const [inline, virtual]

Returns true if the feature is broken.

Returns:
True if the feature is broken

Definition at line 307 of file gnBaseFeature.h.
References m_broken.

boolean gnBaseFeature::IsContainedBy ( const gnLocation & l ) const [virtual]

Checks if this feature is entirely contained by the given location.

Parameters:

l The location to check

Returns:
True if "l" contains by this feature. False otherwise

Definition at line 158 of file gnBaseFeature.cpp.
References gnLocation::Contains(), m_locationList, and uint32.
Referenced by gnGenomeSpec::AddFeature().

uint32 gnBaseFeature::LastIndexOfQualifier ( const string & name,

uint32 listI

) const [virtual]

Searches for a qualifier by name, ending at the index listI.

Parameters:

name The name of the qualifier to look for.

listI The index into the qualifier list to end the search at.

Returns:
The index of the qualifier.

Definition at line 86 of file gnBaseFeature.cpp.
References GNSEQI_END, m_qualifierList, and uint32.

boolean gnBaseFeature::MoveNegative ( const gnSeqI i ) [virtual]

Decreases this feature's coordinates by a specific number of bases.

Parameters:

i The number of bases to decrease by.

Returns:
True if successful, false if the feature was broken by the change.

Definition at line 49 of file gnBaseFeature.cpp.
References m_locationList, and uint32.

boolean gnBaseFeature::MovePositive ( const gnSeqI i ) [virtual]

Increases this feature's coordinates by a specific number of bases.

Parameters:

i The number of bases to increase by.

Returns:
True if successful, false if the feature was broken by the change.

Definition at line 41 of file gnBaseFeature.cpp.
References m_locationList, and uint32.
Referenced by gnGenomeSpec::GetFeature().

boolean gnBaseFeature::RemoveLocation ( uint32 listI ) [virtual]

Deletes the location at listI.

Parameters:

listI The index into the location list to delete.

Returns:
True if successful, false otherwise.

Definition at line 200 of file gnBaseFeature.cpp.
References m_locationList.

boolean gnBaseFeature::RemoveQualifier ( uint32 listI ) [virtual]

Deletes the qualifier at the list index listI.

Parameters:

listI The index into the qualifier list.

Returns:
True if successful, false otherwise.

Definition at line 96 of file gnBaseFeature.cpp.
References m_qualifierList.

void gnBaseFeature::SetBroken ( boolean broke ) [inline, virtual]

Sets whether the feature is broken or not.

Parameters:

broke True if the feature should be broken, false otherwise

Definition at line 311 of file gnBaseFeature.h.
References m_broken.

void gnBaseFeature::SetID ( uint32 id ) [inline, virtual]

Sets this feature's ID.

Parameters:

id The feature's ID.

Definition at line 295 of file gnBaseFeature.h.
References m_id.

boolean gnBaseFeature::SetLocation ( const gnLocation & l,

uint32 listI

) [virtual]

Sets the location at listI to a new location.

Parameters:

l The new location

listI The index into the location list to set.

Returns:
True if successful, false otherwise.

Definition at line 208 of file gnBaseFeature.cpp.
References m_locationList.

void gnBaseFeature::SetLocationType ( gnLocation::gnLocationType lType ) [inline, virtual]

Sets this feature's location type.
LT_BetweenBases is not a valid feature location type.
Parameters:

lType The feature's location type.

See also:
gnLocationType

Definition at line 320 of file gnBaseFeature.h.
References m_locationType.
Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

void gnBaseFeature::SetName ( const string & name ) [inline, virtual]

Sets the feature name.

Parameters:

name The feature name.

Definition at line 287 of file gnBaseFeature.h.
References m_name.

boolean gnBaseFeature::SetQualifier ( string & name,

string & value,

uint32 listI

) [virtual]

Set the name and value of the qualifier at the list index listI.

Parameters:

name The new name of the qualifier.

value The new value of the qualifier.

listI The index into the qualifier list.

Returns:
True if successful, false otherwise.

Definition at line 104 of file gnBaseFeature.cpp.
References m_qualifierList.

boolean gnBaseFeature::SetQualifierName ( string & name,

uint32 listI

) [virtual]

Set the name of the qualifier at the list index listI.

Parameters:

name The new name of the qualifier.

listI The index into the qualifier list.

Returns:
True if successful, false otherwise.

Definition at line 112 of file gnBaseFeature.cpp.
References m_qualifierList.

boolean gnBaseFeature::SetQualifierValue ( string & value,

uint32 listI

) [virtual]

Set the value of the qualifier at the list index listI.

Parameters:

value The new value of the qualifier.

listI The index into the qualifier list.

Returns:
True if successful, false otherwise.

Definition at line 121 of file gnBaseFeature.cpp.
References GetName(), and m_qualifierList.

void gnBaseFeature::SetSpec ( gnFragmentSpec * spec ) [inline, virtual]

Sets the gnFragmentSpec to which this feature refers.

Parameters:

spec A pointer to the fragment spec.

Definition at line 303 of file gnBaseFeature.h.
References m_spec.
Referenced by gnFragmentSpec::AddFeature().

Member Data Documentation

boolean gnBaseFeature::m_broken [protected]

Definition at line 275 of file gnBaseFeature.h.
Referenced by gnBaseFeature(), gnFeature::gnFeature(), IsBroken(), and SetBroken().

uint32 gnBaseFeature::m_id [protected]

Definition at line 273 of file gnBaseFeature.h.
Referenced by GetID(), gnBaseFeature(), gnFeature::gnFeature(), and SetID().

vector< gnLocation > gnBaseFeature::m_locationList [protected]

Definition at line 277 of file gnBaseFeature.h.
Referenced by AddLocation(), Contains(), CropEnd(), CropStart(), GetLocation(), GetLocationListLength(), gnFeature::gnFeature(), Intersects(), IsContainedBy(), MoveNegative(), MovePositive(), RemoveLocation(), and SetLocation().

gnLocation::gnLocationType gnBaseFeature::m_locationType [protected]

Definition at line 276 of file gnBaseFeature.h.
Referenced by GetLocationType(), gnBaseFeature(), gnFeature::gnFeature(), and SetLocationType().

string gnBaseFeature::m_name [protected]

Definition at line 274 of file gnBaseFeature.h.
Referenced by GetName(), gnBaseFeature(), gnFeature::gnFeature(), and SetName().

vector< gnBaseQualifier* > gnBaseFeature::m_qualifierList [protected]

Definition at line 278 of file gnBaseFeature.h.
Referenced by AddQualifier(), FirstIndexOfQualifier(), GetQualifier(), GetQualifierListLength(), GetQualifierName(), GetQualifierValue(), gnFeature::gnFeature(), HasQualifier(), LastIndexOfQualifier(), RemoveQualifier(), SetQualifier(), SetQualifierName(), SetQualifierValue(), and ~gnBaseFeature().

gnFragmentSpec* gnBaseFeature::m_spec [protected]

Definition at line 279 of file gnBaseFeature.h.
Referenced by GetSpec(), gnBaseFeature(), gnFeature::gnFeature(), and SetSpec().

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

Generated on Mon Feb 3 02:34:44 2003 for libGenome by

1.3-rc3

gnBaseFeature Class Reference

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation