public final class GenomePosition extends Object implements Serializable, Comparable<GenomePosition>
GenomePosition
.
In the case of one-based position, pos
points to the pos
-th base in string from the left when
starting to count at 1. In the case of zero-based positions, pos
points to the gap left of the character in
the case of positions on the forward strand and to the gap right of the character in the case of positions on the
reverse strand. When interpreting this for the reverse strand (i.e. counting from the right), the position right of a
character is interpreted as the gap before the character.
Reverse-complementing a zero-based GenomePosition must be equivalent to reverse-complementing its one-based position
representation. Thus, they are shifted towards the right gap besides the character they point at when changing the
strand.Constructor and Description |
---|
GenomePosition(GenomePosition other)
construct genome position from other with selected coordinate system
|
GenomePosition(GenomePosition other,
Strand strand)
construct genome position from other with the selected strand
|
GenomePosition(ReferenceDictionary refDict,
Strand strand,
int chr,
int pos)
construct genome position with zero-based coordinate system
|
GenomePosition(ReferenceDictionary refDict,
Strand strand,
int chr,
int pos,
PositionType positionType)
construct genome position with selected coordinate system
|
Modifier and Type | Method and Description |
---|---|
int |
compareTo(GenomePosition other) |
int |
differenceTo(GenomeInterval itv) |
int |
differenceTo(GenomePosition pos) |
boolean |
equals(Object obj) |
int |
getChr() |
int |
getPos() |
ReferenceDictionary |
getRefDict() |
Strand |
getStrand() |
int |
hashCode() |
boolean |
isEq(GenomePosition other) |
boolean |
isGeq(GenomePosition other) |
boolean |
isGt(GenomePosition other) |
boolean |
isLeq(GenomePosition other) |
boolean |
isLt(GenomePosition other) |
GenomePosition |
shifted(int delta)
Return shifted GenomePosition.
|
String |
toString() |
GenomePosition |
withStrand(Strand strand)
convert into GenomePosition of the given strand
|
public GenomePosition(ReferenceDictionary refDict, Strand strand, int chr, int pos)
public GenomePosition(ReferenceDictionary refDict, Strand strand, int chr, int pos, PositionType positionType)
public GenomePosition(GenomePosition other)
public GenomePosition(GenomePosition other, Strand strand)
public ReferenceDictionary getRefDict()
public Strand getStrand()
public int getChr()
public int getPos()
public GenomePosition withStrand(Strand strand)
public boolean isLt(GenomePosition other)
public boolean isLeq(GenomePosition other)
public boolean isGt(GenomePosition other)
public boolean isGeq(GenomePosition other)
public boolean isEq(GenomePosition other)
public int differenceTo(GenomePosition pos)
pos
- other position to compute difference to(this.pos - pos.pos)
(pos
is adjusted to the coordinate system
and strand of this
)InvalidCoordinateException
- if this
and pos
are on different chromosomespublic int differenceTo(GenomeInterval itv)
itv
- interval to compute difference toitv
, as would be returned by
differenceTo(GenomePosition)
), 0
if this
lies in itv
InvalidCoordinateException
- if this
and itv
are on different chromosomespublic GenomePosition shifted(int delta)
delta > 0
and towards the 5' end
otherwise.delta
- the value to add to the positionpublic int compareTo(GenomePosition other)
compareTo
in interface Comparable<GenomePosition>
Copyright © 2016. All rights reserved.