GenomeVariant (Jannovar 0.17 API)

java.lang.Object
- de.charite.compbio.jannovar.reference.GenomeVariant

All Implemented Interfaces:

VariantDescription
```
public final class GenomeVariant
extends Object
implements VariantDescription
```
Denote a change with a "REF" and an "ALT" string using genome coordinates. GenomeChange objects are immutable, the members are automatically adjusted for the longest common suffix and prefix in REF and ALT. Symbolic alleles, as in the VCF standard, are also possible, but methods like getType() etc. do not return sensible results.

Author:

Manuel Holtgrewe, Max Schubach, Peter N Robinson

Constructor Summary

Constructors
Constructor and Description
`GenomeVariant(GenomePosition pos, String ref, String alt)` Construct object given the position, reference, and alternative nucleic acid string.
`GenomeVariant(GenomePosition pos, String ref, String alt, Strand strand)` Construct object given the position, reference, alternative nucleic acid string, and strand.
`GenomeVariant(GenomeVariant other, Strand strand)` Construct object and enforce strand.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(Annotation other)`
`boolean`	`equals(Object obj)`
`String`	`getAlt()`
`int`	`getChr()`
`String`	`getChrName()`
`GenomeInterval`	`getGenomeInterval()`
`GenomePosition`	`getGenomePos()`
`int`	`getPos()`
`String`	`getRef()`
`GenomeVariantType`	`getType()`
`int`	`hashCode()`
`boolean`	`isSymbolic()`
`boolean`	`isTransition()` A transition is between purine and purine or between pyrimidine and pyrimidine.
`boolean`	`isTransversion()` A transversion is purine <-> pyrimidine.
`String`	`toString()`
`GenomeVariant`	`withStrand(Strand strand)`

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - GenomeVariant
```
public GenomeVariant(GenomePosition pos,
                     String ref,
                     String alt)
```
    Construct object given the position, reference, and alternative nucleic acid string. On construction, pos, ref, and alt are automatically adjusted to the right/incremented by the length of the longest common prefix and suffix of ref and alt.
  - GenomeVariant
```
public GenomeVariant(GenomePosition pos,
                     String ref,
                     String alt,
                     Strand strand)
```
    Construct object given the position, reference, alternative nucleic acid string, and strand. On construction, pos, ref, and alt are automatically adjusted to the right/incremented by the length of the longest common prefix and suffix of ref and alt. Further, the position is adjusted to the given strand.
  - GenomeVariant
```
public GenomeVariant(GenomeVariant other,
                     Strand strand)
```
    Construct object and enforce strand.
- Method Detail
  - isSymbolic
```
public boolean isSymbolic()
```
    Returns:
    
    true if this is a symbolic allele, as described
  - getChrName
```
public String getChrName()
```
    Specified by:
    
    getChrName in interface VariantDescription
    
    Returns:
    
    String with the canonical chromosome name
  - getGenomePos
```
public GenomePosition getGenomePos()
```
  - getPos
```
public int getPos()
```
    Specified by:
    
    getPos in interface VariantDescription
    
    Returns:
    
    zero-based position of the variant on the chromosome
  - getRef
```
public String getRef()
```
    Specified by:
    
    getRef in interface VariantDescription
    
    Returns:
    
    String with the reference allele in the variant, without common suffix or prefix to reference allele.
  - getAlt
```
public String getAlt()
```
    Specified by:
    
    getAlt in interface VariantDescription
    
    Returns:
    
    String with the alternative allele in the variant, without common suffix or prefix to reference allele.
  - getChr
```
public int getChr()
```
    Specified by:
    
    getChr in interface VariantDescription
    
    Returns:
    
    numeric ID of chromosome this change is on
  - getGenomeInterval
```
public GenomeInterval getGenomeInterval()
```
    Returns:
    
    interval of the genome change
  - withStrand
```
public GenomeVariant withStrand(Strand strand)
```
    Returns:
    
    the GenomeChange on the given strand
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
    
    Returns:
    
    human-readable String describing the genome change
  - getType
```
public GenomeVariantType getType()
```
    Returns:
    
    the GenomeVariantType of this GenomeChange
  - isTransition
```
public boolean isTransition()
```
    A transition is between purine and purine or between pyrimidine and pyrimidine. Only applies to single nucleotide subsitutions.
    
    Returns:
    
    true if the variant is a SNV and a transition.
  - isTransversion
```
public boolean isTransversion()
```
    A transversion is purine <-> pyrimidine. Only applies to single nucleotide subsitutions.
    
    Returns:
    
    true if the variant is a SNV and a transversion.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - compareTo
```
public int compareTo(Annotation other)
```
    Specified by:
    
    compareTo in interface VariantDescription

Class GenomeVariant

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

GenomeVariant

GenomeVariant

GenomeVariant

Method Detail

isSymbolic

getChrName

getGenomePos

getPos

getRef

getAlt

getChr

getGenomeInterval

withStrand

toString

getType

isTransition

isTransversion

hashCode

equals

compareTo