org.utgenome.util.sv
Class GeneticVariation

java.lang.Object
  extended by org.utgenome.util.sv.GeneticVariation
Direct Known Subclasses:
EnhancedGeneticVariation

public class GeneticVariation
extends Object

genetic variation location [start, end), chr and allele (genotype) information

Author:
leo

Nested Class Summary
static class GeneticVariation.VariationType
           
 
Field Summary
 String chr
           
 int indelLength
           
 String refBase
           
 int start
           
 GeneticVariation.VariationType variationType
           
 
Constructor Summary
GeneticVariation()
           
GeneticVariation(GeneticVariation other)
           
GeneticVariation(String chr, int start, String genotype)
           
 
Method Summary
 IUPAC getAltBase()
           
 String getGenotype()
           
 void setGenotype(String genotype)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

variationType

public GeneticVariation.VariationType variationType

chr

public String chr

start

public int start

refBase

public String refBase

indelLength

public int indelLength
Constructor Detail

GeneticVariation

public GeneticVariation()

GeneticVariation

public GeneticVariation(String chr,
                        int start,
                        String genotype)
Parameters:
type -
chr -
start - 1-origin (inclusive)
end - 1-origin (exclusive)
genotype - A, C, AC, ACGT (genotype), *, +A (insertion to reference), -aatT (deletion from reference), etc.

GeneticVariation

public GeneticVariation(GeneticVariation other)
Method Detail

getAltBase

public IUPAC getAltBase()

getGenotype

public String getGenotype()

setGenotype

public void setGenotype(String genotype)

toString

public String toString()
Overrides:
toString in class Object


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