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
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
A symbol representing a position that falls in between two bases, eg. 2^3 falls somewhere in the gap between 2 and 3.static final Position
The empty position lies nowhere.static final String
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
Modifier and TypeMethodDescriptionint
getEnd()
Returns the end of the range of bases this base could lie in.boolean
Returns true if the position has a fuzzy end.boolean
Returns true if the position has a fuzzy start.int
getStart()
Returns the beginning of the range of bases this base could lie in.getType()
Returns the type of this position if it is not a point/single position.translate
(int distance) Takes this position and returns a copy translated by 'distance' bases.
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Field Details
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EMPTY_POSITION
The empty position lies nowhere. -
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:
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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:
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Method Details
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getFuzzyStart
boolean getFuzzyStart()Returns true if the position has a fuzzy start.- Returns:
- the fuzziness of the start.
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getFuzzyEnd
boolean getFuzzyEnd()Returns true if the position has a fuzzy end.- Returns:
- the fuzziness of the end.
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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.
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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.
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translate
Takes this position and returns a copy translated by 'distance' bases.- Parameters:
distance
- the distance to translate it.- Returns:
- the translated position.
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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.
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