Package org.snpeff.interval
Class Interval
java.lang.Object
org.snpeff.interval.Interval
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
- Direct Known Subclasses:
Marker
A genomic interval.
Note: Intervals are assumed to be zero-based and inclusive i.e. an interval including the first base up to base X would be [0,X] NOT [1,X]
- Author:
- pcingola
- See Also:
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionclone()
int
Compare by start and endboolean
findParent
(Class clazz) Go up (parent) until we find an instance of 'clazz'Find chromosome namedouble
Find chromosome and return it's numberint
getEnd()
Find genomeFind genome namegetId()
int
getStart()
int
hashCode()
boolean
intersects
(int iStart, int iEnd) Return true if this intersects '[iStart, iEnd]'boolean
intersects
(long point) boolean
intersects
(Interval interval) Return true if this intersects 'interval'boolean
intersects
(Marker interval) Do the intervals intersect?int
intersectSize
(Marker interval) How much do intervals intersect?boolean
Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?boolean
isSameChromo
(Marker interval) boolean
boolean
boolean
isValid()
void
setChromosomeNameOri
(String chromosomeNameOri) void
setEnd
(int end) void
void
void
setStart
(int start) void
setStrandMinus
(boolean strand) void
shiftCoordinates
(int shift) int
size()
toStr()
To string as a simple "chr:start-end" formattoString()
toStringAsciiArt
(int maxLen) Show it as an ASCII arttoStrPos()
To string as a simple "chr:start-end" format
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Field Details
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start
protected int start -
end
protected int end -
strandMinus
protected boolean strandMinus -
id
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chromosomeNameOri
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parent
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Constructor Details
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Interval
protected Interval() -
Interval
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Method Details
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clone
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compareTo
Compare by start and end- Specified by:
compareTo
in interfaceComparable<Interval>
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equals
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findParent
Go up (parent) until we find an instance of 'clazz' -
getChromosome
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getChromosomeName
Find chromosome name -
getChromosomeNameOri
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setChromosomeNameOri
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getChromosomeNum
public double getChromosomeNum()Find chromosome and return it's number- Returns:
- Chromosome number if found, -1 otherwise
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getEnd
public int getEnd() -
setEnd
public void setEnd(int end) -
getGenome
Find genome -
getGenomeName
Find genome name -
getId
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setId
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getParent
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setParent
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getStart
public int getStart() -
setStart
public void setStart(int start) -
getStrand
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hashCode
public int hashCode() -
intersects
public boolean intersects(int iStart, int iEnd) Return true if this intersects '[iStart, iEnd]' -
intersects
Return true if this intersects 'interval' -
intersects
public boolean intersects(long point) - Returns:
- true if this interval contains point (inclusive)
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intersects
Do the intervals intersect?- Returns:
- return true if this intersects 'interval'
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intersectSize
How much do intervals intersect?- Returns:
- number of bases these intervals intersect
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isCircular
public boolean isCircular()Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line? -
isSameChromo
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isStrandMinus
public boolean isStrandMinus() -
setStrandMinus
public void setStrandMinus(boolean strand) -
isStrandPlus
public boolean isStrandPlus() -
isValid
public boolean isValid() -
shiftCoordinates
public void shiftCoordinates(int shift) -
size
public int size() -
toStr
To string as a simple "chr:start-end" format -
toString
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toStringAsciiArt
Show it as an ASCII art -
toStrPos
To string as a simple "chr:start-end" format
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