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

Fields

Modifier and Type	Field and Description
static 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.
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. 5.10 falls on some base between 5 and 10.

Method Summary

Methods

Modifier and Type	Method and Description
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.