org.biojavax.bio.seq
Interface Position

All Known Implementing Classes:

SimplePosition

public interface Position

Holds info about base positions.

Since:

1.5

Author:

Richard Holland

Field Summary

static String	BETWEEN_BASES A symbol representing a position that falls in between two bases, eg.
static Position	EMPTY_POSITION The empty position lies nowhere.
static String	IN_RANGE A symbol representing a position that occupies a single base somewhere in a range, eg.

Method Summary

int	getEnd() Returns the end of the range of bases this base could lie in.
boolean	getFuzzyEnd() Returns true if the position has a fuzzy end.
boolean	getFuzzyStart() Returns true if the position has a fuzzy start.
int	getStart() Returns the beginning of the range of bases this base could lie in.
String	getType() Returns the type of this position if it is not a point/single position.
Position	translate(int distance) Takes this position and returns a copy translated by 'distance' bases.

Field Detail

EMPTY_POSITION

static final Position EMPTY_POSITION

The empty position lies nowhere.

BETWEEN_BASES

static final String BETWEEN_BASES

A symbol representing a position that falls in between two bases, eg. 2^3 falls somewhere in the gap between 2 and 3.

See Also:

Constant Field Values

IN_RANGE

static final String IN_RANGE

A symbol representing a position that occupies a single base somewhere in a range, eg. 5.10 falls on some base between 5 and 10.

See Also:

Constant Field Values

Method Detail

getFuzzyStart

boolean getFuzzyStart()

Returns true if the position has a fuzzy start.

Returns:

the fuzziness of the start.

getFuzzyEnd

boolean getFuzzyEnd()

Returns true if the position has a fuzzy end.

Returns:

the fuzziness of the end.

getStart

int getStart()

Returns the beginning of the range of bases this base could lie in. If this position is a single position, then start=end.

Returns:

the start of this position.

getEnd

int getEnd()

Returns the end of the range of bases this base could lie in. If this position is a single position, then start=end.

Returns:

the end of this position.

translate

Position translate(int distance)

Takes this position and returns a copy translated by 'distance' bases.

Parameters:

distance - the distance to translate it.

Returns:

the translated position.

getType

String getType()

Returns the type of this position if it is not a point/single position. Types are usually BETWEEN_BASES or IN_RANGE but could be any string value.

Returns:

the type of this position.