net.maizegenetics.dna.map

Class GeneralPosition

net.maizegenetics.dna.map.GeneralPosition

All Implemented Interfaces:

Position

public class GeneralPosition
implements Position

Provide information on a site and its annotations. This includes information on position, MAF, coverage. This class is immutable.

The annotations are all set using the builder.

This class has been optimized for memory size compared to the other version. Every annotated position takes about 84 bytes, even with a names and declared variants. Positions with extended annotation take roughly 117 bytes, and as long as the annotation are repeated extensively the take an additional 8 bytes each. So a site with 100 annotation would take <1000 bytes.

Method Detail

equals

public boolean equals(java.lang.Object obj)

compareTo

public int compareTo(Position o)

toString

public java.lang.String toString()

getGlobalMAF

public float getGlobalMAF()

getGlobalSiteCoverage

public float getGlobalSiteCoverage()

getAllele

public byte getAllele(WHICH_ALLELE alleleType)

hashCode

public int hashCode()

getChromosome

public Chromosome getChromosome()

getPosition

public int getPosition()

getInsertionPosition

public short getInsertionPosition()

getStrand

public byte getStrand()

getStrandStr

public java.lang.String getStrandStr()

getSNPID

public java.lang.String getSNPID()

getActualSNPID

public java.lang.String getActualSNPID()

isNucleotide

public boolean isNucleotide()

isIndel

public boolean isIndel()

getKnownVariants

public java.lang.String[] getKnownVariants()

getAnnotation

public GeneralAnnotation getAnnotation()