Package 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 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
All Methods Instance Methods Abstract Methods Modifier and Type Method 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.

