Package org.snpeff.interval
Class Interval
- java.lang.Object
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- org.snpeff.interval.Interval
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<Interval>
- Direct Known Subclasses:
Marker
public class Interval extends java.lang.Object implements java.lang.Comparable<Interval>, java.io.Serializable, java.lang.Cloneable
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:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String
chromosomeNameOri
protected int
end
protected java.lang.String
id
protected Interval
parent
protected int
start
protected boolean
strandMinus
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Interval
clone()
int
compareTo(Interval i2)
Compare by start and endboolean
equals(Interval interval)
Interval
findParent(java.lang.Class clazz)
Go up (parent) until we find an instance of 'clazz'Chromosome
getChromosome()
java.lang.String
getChromosomeName()
Find chromosome namejava.lang.String
getChromosomeNameOri()
double
getChromosomeNum()
Find chromosome and return it's numberint
getEnd()
Genome
getGenome()
Find genomejava.lang.String
getGenomeName()
Find genome namejava.lang.String
getId()
Interval
getParent()
int
getStart()
java.lang.String
getStrand()
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
isCircular()
Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?boolean
isSameChromo(Marker interval)
boolean
isStrandMinus()
boolean
isStrandPlus()
boolean
isValid()
void
setChromosomeNameOri(java.lang.String chromosomeNameOri)
void
setEnd(int end)
void
setId(java.lang.String id)
void
setParent(Interval parent)
void
setStart(int start)
void
setStrandMinus(boolean strand)
void
shiftCoordinates(int shift)
int
size()
java.lang.String
toStr()
To string as a simple "chr:start-end" formatjava.lang.String
toString()
java.lang.String
toStringAsciiArt(int maxLen)
Show it as an ASCII artjava.lang.String
toStrPos()
To string as a simple "chr:start-end" format
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Field Detail
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start
protected int start
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end
protected int end
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strandMinus
protected boolean strandMinus
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id
protected java.lang.String id
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chromosomeNameOri
protected java.lang.String chromosomeNameOri
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parent
protected Interval parent
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Constructor Detail
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Interval
protected Interval()
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Interval
public Interval(Interval parent, int start, int end, boolean strandMinus, java.lang.String id)
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Method Detail
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clone
public Interval clone()
- Overrides:
clone
in classjava.lang.Object
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compareTo
public int compareTo(Interval i2)
Compare by start and end- Specified by:
compareTo
in interfacejava.lang.Comparable<Interval>
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equals
public boolean equals(Interval interval)
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findParent
public Interval findParent(java.lang.Class clazz)
Go up (parent) until we find an instance of 'clazz'
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getChromosome
public Chromosome getChromosome()
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getChromosomeName
public java.lang.String getChromosomeName()
Find chromosome name
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getChromosomeNameOri
public java.lang.String getChromosomeNameOri()
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setChromosomeNameOri
public void setChromosomeNameOri(java.lang.String chromosomeNameOri)
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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()
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setEnd
public void setEnd(int end)
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getGenome
public Genome getGenome()
Find genome
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getGenomeName
public java.lang.String getGenomeName()
Find genome name
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getId
public java.lang.String getId()
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setId
public void setId(java.lang.String id)
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getParent
public Interval getParent()
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setParent
public void setParent(Interval parent)
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getStart
public int getStart()
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setStart
public void setStart(int start)
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getStrand
public java.lang.String getStrand()
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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intersects
public boolean intersects(int iStart, int iEnd)
Return true if this intersects '[iStart, iEnd]'
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intersects
public boolean intersects(Interval interval)
Return true if this intersects 'interval'
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intersects
public boolean intersects(long point)
- Returns:
- true if this interval contains point (inclusive)
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intersects
public boolean intersects(Marker interval)
Do the intervals intersect?- Returns:
- return true if this intersects 'interval'
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intersectSize
public int intersectSize(Marker interval)
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?
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isSameChromo
public boolean isSameChromo(Marker interval)
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isStrandMinus
public boolean isStrandMinus()
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setStrandMinus
public void setStrandMinus(boolean strand)
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isStrandPlus
public boolean isStrandPlus()
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isValid
public boolean isValid()
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shiftCoordinates
public void shiftCoordinates(int shift)
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size
public int size()
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toStr
public java.lang.String toStr()
To string as a simple "chr:start-end" format
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toStringAsciiArt
public java.lang.String toStringAsciiArt(int maxLen)
Show it as an ASCII art
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toStrPos
public java.lang.String toStrPos()
To string as a simple "chr:start-end" format
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