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gnLocation Class Reference

This class is used to store sequence locations. More...

#include <gnLocation.h>

Inheritance diagram for gnLocation::

Public Types
enum	intersectRestriction { determinedRegions, undeterminedRegions, allRegions }
enum	gnLocationType { LT_Standard, LT_BetweenBases, LT_Complement, LT_Order, LT_Group, LT_OneOf, LT_Nothing }
Public Methods
	gnLocation ()
	Empty constructor, does nothing. More...
	gnLocation (const gnLocation &s)
	Copy constructor, copies a gnLocation. More...
	gnLocation (const gnSeqI start, const gnSeqI end, const gnLocationType type=LT_Standard, string contigName="")
	Constructor, creates a gnLocation. More...
	gnLocation (const gnSeqI start, const gnSeqI startLength, const gnSeqI end, gnSeqI endLength, const gnLocationType type=LT_Standard, string contigName="")
	Constructor, creates a gnLocation. More...
gnLocation*	Clone () const
void	Clear ()
	Resets this location to default values. More...
boolean	CropTo (const gnLocation &l)
	Crops this location to fit within the specified location boundaries. More...
boolean	CropStart (const gnSeqI start)
	Crops the start location by the specified amount. More...
boolean	CropEnd (const gnSeqI end)
	Crops the end location by the specified amount. More...
boolean	Intersects (const gnLocation &l, const intersectRestriction ir=allRegions) const
	Returns true if the given location intersects this location in the region specified by the parameter "ir". More...
boolean	Contains (const gnLocation &l, const intersectRestriction cr=allRegions) const
	Crops the end location by the specified amount. More...
boolean	MovePositive (const gnSeqI diff)
	Increases the location start and end. More...
boolean	MoveNegative (const gnSeqI diff)
	Decreases the location start and end. More...
boolean	MoveTo (const int direction, const gnSeqI diff)
	Moves the location start and end. More...
gnSeqI	GetEnd () const
	Gets the ending base pair. More...
gnSeqI	GetEndLength () const
	Gets the ending base pair's definition value. More...
gnSeqI	GetLast () const
gnSeqI	GetStart () const
	Gets the starting base pair. More...
gnSeqI	GetStartLength () const
	Gets the starting base pair's definition value. More...
gnSeqI	GetFirst () const
gnLocationType	GetType () const
	Gets the location type. More...
void	GetBounds (gnSeqI &s, gnSeqI &sl, gnSeqI &e, gnSeqI &el) const
	Gets the location's boundaries. More...
bool	IsEndBoundLonger () const
	Returns true if the end is unbounded to the right. More...
bool	IsStartBoundLonger () const
	Returns true if the start is unbounded to the right. More...
bool	IsEndBoundShorter () const
	Returns true if the end is unbounded to the left. More...
bool	IsStartBoundShorter () const
	Returns true if the start is unbounded to the left. More...
void	SetEnd (const gnSeqI end)
	Sets the end location. More...
void	SetEnd (const gnSeqI end, const gnSeqI endLength)
	Sets the end location and definition. More...
void	SetEndLength (const gnSeqI endLength)
	Sets the end definition. More...
void	SetStart (const gnSeqI start)
	Sets the start location/. More...
void	SetStart (const gnSeqI start, const gnSeqI startLength)
	Sets the start location and definition. More...
void	SetStartLength (const gnSeqI startLength)
	Sets the start definition. More...
void	SetType (const gnLocationType lt)
	Sets the location type. More...
void	SetBounds (const gnSeqI start, const gnSeqI startLength, const gnSeqI end, const gnSeqI endLength)
	Sets the location's boundaries. More...
void	SetBounds (const gnSeqI start, const gnSeqI end)
	Sets the location's boundaries. More...
gnLocation	GetUnion (const gnLocation &l) const
gnLocation	GetIntersection (const gnLocation &l, const intersectRestriction ir) const
Static Public Attributes
const gnSeqI	Defined = 0
const gnSeqI	Unknown = GNSEQI_END
Private Attributes
string	m_name
gnSeqI	m_start
gnSeqI	m_startLength
gnSeqI	m_end
gnSeqI	m_endLength
gnLocationType	m_type

Detailed Description

This class is used to store sequence locations.

gnBaseFeature uses it to track feature locations. gnLocation is capable of representing any GenBank style location qualifier. gnLocation stores the start coordinate and a startLength value which represents the length of an undetermined region of sequence prior to the starting coordinate. A startLength of GNSEQI_END represents an unknown start, whereas a startLength of 0 implies that the start coordinate is unambiguous. Any value other value indicates a range of coordinates for the starting position. The range is bounded by the given start coordinate and extends startLength characters upstream. Likewise, an endLength of GNSEQI_END represents an unknown ambiguous end coordinate, and an endLength of 0 implies that the end coordinate is unambiguous. Any other value for endLength denotes a range of ending coordinates starting at end and continuing for endLength characters.

Definition at line 37 of file gnLocation.h.

Member Enumeration Documentation

enum gnLocation::gnLocationType

Enumeration values:

LT_Standard

LT_BetweenBases

LT_Complement

LT_Order

LT_Group

LT_OneOf

LT_Nothing

Definition at line 46 of file gnLocation.h.

enum gnLocation::intersectRestriction

Enumeration values:

determinedRegions

undeterminedRegions

allRegions

Definition at line 40 of file gnLocation.h.

Constructor & Destructor Documentation

gnLocation::gnLocation ( )

Empty constructor, does nothing.

Definition at line 16 of file gnLocation.cpp.
Referenced by Clone().

gnLocation::gnLocation ( const gnLocation & s )

Copy constructor, copies a gnLocation.

Parameters:

s the location to copy.

Definition at line 20 of file gnLocation.cpp.

gnLocation::gnLocation ( const gnSeqI start,

const gnSeqI end,

const gnLocationType type = LT_Standard,

string contigName = "" )

Constructor, creates a gnLocation.

Parameters:

start The start position within the sequence.

end The end position within the sequence.

type The type of the location, LT_Standard by default.

contigName The name of the contig associated with this location, empty by default.

See also:
gnLocationType

Definition at line 31 of file gnLocation.cpp.

gnLocation::gnLocation ( const gnSeqI start,

const gnSeqI startLength,

const gnSeqI end,

gnSeqI endLength,

const gnLocationType type = LT_Standard,

string contigName = "" )

Constructor, creates a gnLocation.

Parameters:

start The start position within the sequence.

startLength GNSEQI_END if the starting location is unbounded to the left, 0 if defined, otherwise it specifies a range

end The end position within the sequence.

endLength 0 if defined, GNSEQI_END if unbounded to the right, otherwise specifies a range

type The type of the location, LT_Standard by default.

contigName The name of the contig associated with this location, empty by default.

See also:
gnLocationType

Definition at line 25 of file gnLocation.cpp.

Member Function Documentation

void gnLocation::Clear ( )

Resets this location to default values.

Definition at line 43 of file gnLocation.cpp.
Referenced by CropTo(), and gnLocation().

gnLocation * gnLocation::Clone ( ) const [virtual]

Reimplemented from gnClone.
Definition at line 38 of file gnLocation.cpp.

boolean gnLocation::Contains ( const gnLocation & l,

const intersectRestriction cr = allRegions ) const

Crops the end location by the specified amount.

Parameters:

end The amount to crop.

Returns:
True if the location still exists, false if the crop amount is larger than the location.

Definition at line 166 of file gnLocation.cpp.
Referenced by gnBaseFeature::Contains(), and gnBaseFeature::IsContainedBy().

boolean gnLocation::CropEnd ( const gnSeqI end )

Crops the end location by the specified amount.

Parameters:

end The amount to crop.

Returns:
True if the location still exists, false if the crop amount is larger than the location.

Definition at line 131 of file gnLocation.cpp.
Referenced by gnBaseFeature::CropEnd(), gnGenomeSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), and gnGenomeSpec::GetIntersectingFeatures().

boolean gnLocation::CropStart ( const gnSeqI start )

Crops the start location by the specified amount.

Parameters:

start The amount to crop.

Returns:
True if the location still exists, false if the crop amount is larger than the location.

Definition at line 119 of file gnLocation.cpp.
Referenced by gnBaseFeature::CropStart().

boolean gnLocation::CropTo ( const gnLocation & l )

Crops this location to fit within the specified location boundaries.

Parameters:

l The location boundaries.

Returns:
True if the location still exists, false if the crop amount is larger than the location.

Definition at line 72 of file gnLocation.cpp.

void gnLocation::GetBounds ( gnSeqI & s,

gnSeqI & sl,

gnSeqI & e,

gnSeqI & el ) const

Gets the location's boundaries.

Parameters:

s The start index.

sl The start length.

e The end index.

el The end length.

Definition at line 53 of file gnLocation.cpp.

gnSeqI gnLocation::GetEnd ( ) const [inline]

Gets the ending base pair.

Returns:
The ending base pair.

Definition at line 275 of file gnLocation.h.
Referenced by gnBaseFeature::Contains(), gnBaseFeature::Crop(), CropTo(), LocationEndLessthan(), LocationSizeLessthan(), and gnGBKSource::Write().

gnSeqI gnLocation::GetEndLength ( ) const [inline]

Gets the ending base pair's definition value.

Returns:
-1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right

Definition at line 280 of file gnLocation.h.

gnSeqI gnLocation::GetFirst ( ) const [inline]

Definition at line 301 of file gnLocation.h.
Referenced by Contains(), CropTo(), GetIntersection(), and Intersects().

gnLocation gnLocation::GetIntersection ( const gnLocation & l,

const intersectRestriction ir ) const

Definition at line 207 of file gnLocation.cpp.

gnSeqI gnLocation::GetLast ( ) const [inline]

Definition at line 285 of file gnLocation.h.
Referenced by Contains(), CropTo(), GetIntersection(), and Intersects().

gnSeqI gnLocation::GetStart ( ) const [inline]

Gets the starting base pair.

Returns:
The starting base pair.

Definition at line 291 of file gnLocation.h.
Referenced by gnBaseFeature::Contains(), gnBaseFeature::Crop(), CropTo(), LocationEndLessthan(), LocationLessthan(), LocationSizeLessthan(), gnGBKSource::Write(), and loc_binary_search().

gnSeqI gnLocation::GetStartLength ( ) const [inline]

Gets the starting base pair's definition value.

Returns:
-1 if the starting location is unbounded to the left, 0 if defined, 1 if unbounded to the right

Definition at line 296 of file gnLocation.h.

gnLocation::gnLocationType gnLocation::GetType ( ) const [inline]

Gets the location type.

Returns:
the location type.
See also:
gnLocationType

Definition at line 307 of file gnLocation.h.
Referenced by gnGBKSource::Write().

gnLocation gnLocation::GetUnion ( const gnLocation & l ) const

Definition at line 200 of file gnLocation.cpp.

boolean gnLocation::Intersects ( const gnLocation & l,

const intersectRestriction ir = allRegions ) const

Returns true if the given location intersects this location in the region specified by the parameter "ir".

Parameters:

l The location to check for intersection.

ir The region to check for intersection. This can be either determinedRegions, undeterminedRegions, or allRegions

Returns:
True if the location still exists, false if the crop amount is larger than the location.

Definition at line 144 of file gnLocation.cpp.
Referenced by gnBaseFeature::Intersects().

bool gnLocation::IsEndBoundLonger ( ) const [inline]

Returns true if the end is unbounded to the right.

Returns:
True if the end is unbounded to the right.

Definition at line 313 of file gnLocation.h.
Referenced by gnGBKSource::Write().

bool gnLocation::IsEndBoundShorter ( ) const [inline]

Returns true if the end is unbounded to the left.

Returns:
True if the end is unbounded to the left.

Definition at line 323 of file gnLocation.h.
Referenced by gnGBKSource::Write().

bool gnLocation::IsStartBoundLonger ( ) const [inline]

Returns true if the start is unbounded to the right.

Returns:
True if the start is unbounded to the right.

Definition at line 318 of file gnLocation.h.
Referenced by gnGBKSource::Write().

bool gnLocation::IsStartBoundShorter ( ) const [inline]

Returns true if the start is unbounded to the left.

Returns:
True if the start is unbounded to the left.

Definition at line 328 of file gnLocation.h.
Referenced by gnGBKSource::Write().

boolean gnLocation::MoveNegative ( const gnSeqI diff )

Decreases the location start and end.

Parameters:

diff The amount to decrease the location start and end.

Definition at line 185 of file gnLocation.cpp.
Referenced by gnGenomeSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnGenomeSpec::GetIntersectingFeatures(), gnBaseFeature::MoveNegative(), and MoveTo().

boolean gnLocation::MovePositive ( const gnSeqI diff )

Increases the location start and end.

Parameters:

diff The amount to increase the location start and end.

Definition at line 177 of file gnLocation.cpp.
Referenced by gnBaseFeature::MovePositive(), and MoveTo().

boolean gnLocation::MoveTo ( const int direction,

const gnSeqI diff )

Moves the location start and end.

Parameters:

direction Negative integer will decrease start and end, positive will increase them.

diff The amount to move the location start and end.

Definition at line 193 of file gnLocation.cpp.

void gnLocation::SetBounds ( const gnSeqI start,

const gnSeqI end )

Sets the location's boundaries.

Parameters:

start The start index.

end The end index.

Definition at line 66 of file gnLocation.cpp.

void gnLocation::SetBounds ( const gnSeqI start,

const gnSeqI startLength,

const gnSeqI end,

const gnSeqI endLength )

Sets the location's boundaries.

Parameters:

start The start index.

startLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right

end The end index.

endLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right

Definition at line 61 of file gnLocation.cpp.
Referenced by gnLocation().

void gnLocation::SetEnd ( const gnSeqI end,

const gnSeqI endLength ) [inline]

Sets the end location and definition.

Parameters:

end The end location.

endLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right

Definition at line 339 of file gnLocation.h.

void gnLocation::SetEnd ( const gnSeqI end ) [inline]

Sets the end location.

Parameters:

end The end location.

Definition at line 334 of file gnLocation.h.
Referenced by gnFragmentSpec::CloneRange(), ComplementLocation(), and SetBounds().

void gnLocation::SetEndLength ( const gnSeqI endLength ) [inline]

Sets the end definition.

Parameters:

endLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right

Definition at line 345 of file gnLocation.h.

void gnLocation::SetStart ( const gnSeqI start,

const gnSeqI startLength ) [inline]

Sets the start location and definition.

Parameters:

start The end location.

startLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right

Definition at line 355 of file gnLocation.h.

void gnLocation::SetStart ( const gnSeqI start ) [inline]

Sets the start location/.

Parameters:

end The start location.

Definition at line 350 of file gnLocation.h.
Referenced by gnFragmentSpec::CloneRange(), ComplementLocation(), and SetBounds().

void gnLocation::SetStartLength ( const gnSeqI startLength ) [inline]

Sets the start definition.

Parameters:

startLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right

Definition at line 361 of file gnLocation.h.

void gnLocation::SetType ( const gnLocationType lt ) [inline]

Sets the location type.

Parameters:

lt The location type.

Definition at line 367 of file gnLocation.h.

Member Data Documentation

const gnSeqI gnLocation::Defined = 0 [static]

Definition at line 56 of file gnLocation.h.

const gnSeqI gnLocation::Unknown = GNSEQI_END [static]

Definition at line 57 of file gnLocation.h.

gnSeqI gnLocation::m_end [private]

Definition at line 266 of file gnLocation.h.

gnSeqI gnLocation::m_endLength [private]

Definition at line 267 of file gnLocation.h.

string gnLocation::m_name [private]

Definition at line 263 of file gnLocation.h.

gnSeqI gnLocation::m_start [private]

Definition at line 264 of file gnLocation.h.

gnSeqI gnLocation::m_startLength [private]

Definition at line 265 of file gnLocation.h.

gnLocationType gnLocation::m_type [private]

Definition at line 269 of file gnLocation.h.

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

Generated at Thu Apr 4 01:45:20 2002 for libGenome by

gnLocation Class Reference

Public Types

Public Methods

Static Public Attributes

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation