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

Constructor & Destructor Documentation

gnBaseFeature::gnBaseFeature ( )

Definition at line 19 of file gnBaseFeature.cpp.

gnBaseFeature::gnBaseFeature ( string & name,

uint32 id = 0,

gnFragmentSpec * spec = NULL,

gnLocation::gnLocationType lt = gnLocation::LT_Nothing,

boolean broken = false )

Definition at line 27 of file gnBaseFeature.cpp.

gnBaseFeature::~gnBaseFeature ( )

Destructor, frees memory.

Definition at line 35 of file gnBaseFeature.cpp.

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 185 of file gnBaseFeature.cpp.
Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

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

Adds a new qualifier.

Parameters:

l The qualifier to add.

Returns:
True if successful, false otherwise.

Definition at line 215 of file gnBaseFeature.cpp.
Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream().

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

Reimplemented from gnClone.
Reimplemented in gnFeature.
Referenced by gnFragmentSpec::GetFeature().

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 145 of file gnBaseFeature.cpp.

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 138 of file gnBaseFeature.cpp.

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 130 of file gnBaseFeature.cpp.

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 329 of file gnBaseFeature.h.

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

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

Parameters:

end The amount to crop.

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

Definition at line 59 of file gnBaseFeature.cpp.
Referenced by Crop(), and gnFragmentSpec::CropEnd().

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 68 of file gnBaseFeature.cpp.
Referenced by Crop(), and gnFragmentSpec::CropStart().

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 75 of file gnBaseFeature.cpp.

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

Gets this feature's ID.

Returns:
The feature's ID.

Definition at line 292 of file gnBaseFeature.h.

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 193 of file gnBaseFeature.cpp.
Referenced by Contains(), Intersects(), gnGBKSource::Write(), and main().

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 325 of file gnBaseFeature.h.
Referenced by Contains(), Intersects(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), gnGBKSource::Write(), and main().

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 317 of file gnBaseFeature.h.
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 284 of file gnBaseFeature.h.
Referenced by SetQualifierValue(), gnGBKSource::Write(), and main().

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 242 of file gnBaseFeature.cpp.
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 333 of file gnBaseFeature.h.
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 230 of file gnBaseFeature.cpp.

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 236 of file gnBaseFeature.cpp.
Referenced by print_feature().

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 300 of file gnBaseFeature.h.

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 223 of file gnBaseFeature.cpp.

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 172 of file gnBaseFeature.cpp.

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 165 of file gnBaseFeature.cpp.
Referenced by gnFragmentSpec::GetIntersectingFeatures().

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

Returns true if the feature is broken.

Returns:
True if the feature is broken

Definition at line 308 of file gnBaseFeature.h.
Referenced by gnFragmentSpec::GetBrokenFeatures().

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 157 of file gnBaseFeature.cpp.
Referenced by gnGenomeSpec::AddFeature(), gnFragmentSpec::GetBrokenFeatures(), and gnFragmentSpec::GetContainedFeatures().

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 87 of file gnBaseFeature.cpp.

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 50 of file gnBaseFeature.cpp.

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 42 of file gnBaseFeature.cpp.
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 199 of file gnBaseFeature.cpp.

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 97 of file gnBaseFeature.cpp.

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 312 of file gnBaseFeature.h.

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

Sets this feature's ID.

Parameters:

id The feature's ID.

Definition at line 296 of file gnBaseFeature.h.

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 207 of file gnBaseFeature.cpp.

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 321 of file gnBaseFeature.h.
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 288 of file gnBaseFeature.h.

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.

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 111 of file gnBaseFeature.cpp.

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 120 of file gnBaseFeature.cpp.

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 304 of file gnBaseFeature.h.
Referenced by gnFragmentSpec::AddFeature().

Member Data Documentation

boolean gnBaseFeature::m_broken [protected]

Definition at line 276 of file gnBaseFeature.h.

uint32 gnBaseFeature::m_id [protected]

Definition at line 274 of file gnBaseFeature.h.

vector< gnLocation > gnBaseFeature::m_locationList< gnLocation > [protected]

Definition at line 278 of file gnBaseFeature.h.

gnLocation::gnLocationType gnBaseFeature::m_locationType [protected]

Definition at line 277 of file gnBaseFeature.h.

string gnBaseFeature::m_name [protected]

Definition at line 275 of file gnBaseFeature.h.

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

Definition at line 279 of file gnBaseFeature.h.

gnFragmentSpec * gnBaseFeature::m_spec [protected]

Definition at line 280 of file gnBaseFeature.h.

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

Generated at Thu Apr 4 01:52:04 2002 for libGenome by

gnBaseFeature Class Reference

Public Methods

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation