net.maizegenetics.dna.map

Class GeneralPosition.Builder

net.maizegenetics.dna.map.GeneralPosition.Builder

Enclosing class:

GeneralPosition

public static class GeneralPosition.Builder

A builder for creating immutable CoreAnnotatedPosition instances. AnnotatedPositions are built off a base of a CorePosition, so build it first.

Example:

   Position cp= new CorePosition.Builder(new Chromosome("1"),1232).build();
      CoreAnnotatedPosition ap= new CoreAnnotatedPosition.Builder(cp)
         .maf(0.05f)
         .ancAllele(NucleotideAlignmentConstants.C_ALLELE)
         .build();

This would create nucleotide position on chromosome 1 at position 1232. The MAF is 0.05 and the ancestral allele is C.

Constructor Detail

Builder

public Builder(Chromosome chr,
               int position)

Constructor requires a Position before annotation of the position

See Also:

Position#of(String, int), Position#builder(String, int)

Builder

public Builder(Chromosome chr,
               int position,
               net.maizegenetics.util.GeneralAnnotationStorage.Builder annotationBuilder)

Builder

public Builder(Position aCorePosition)

Constructor from an existing position

Method Detail

chromosome

public net.maizegenetics.dna.map.GeneralPosition.Builder chromosome(Chromosome val)

Set Chromosome

position

public net.maizegenetics.dna.map.GeneralPosition.Builder position(int val)

Set Position in Chromosome

insertionPosition

public net.maizegenetics.dna.map.GeneralPosition.Builder insertionPosition(short val)

Set Insertion-position

strand

public net.maizegenetics.dna.map.GeneralPosition.Builder strand(byte val)

Set strand (default=1)

strand

public net.maizegenetics.dna.map.GeneralPosition.Builder strand(java.lang.String val)

snpName

public net.maizegenetics.dna.map.GeneralPosition.Builder snpName(java.lang.String val)

Set SNP name (default="S"+Chromosome+"_"+position)

nucleotide

public net.maizegenetics.dna.map.GeneralPosition.Builder nucleotide(boolean val)

Set whether position is nucleotide (default=true)

indel

public net.maizegenetics.dna.map.GeneralPosition.Builder indel(boolean val)

Set whether position is indel (default=false)

knownVariants

public net.maizegenetics.dna.map.GeneralPosition.Builder knownVariants(java.lang.String[] val)

Set text definition of variants (default=null)

knownVariants

public net.maizegenetics.dna.map.GeneralPosition.Builder knownVariants(java.lang.String val)

Set text definition of variants (default=null)

maf

public net.maizegenetics.dna.map.GeneralPosition.Builder maf(float val)

Set Minor Allele Frequency annotation (default=Float.NaN)

siteCoverage

public net.maizegenetics.dna.map.GeneralPosition.Builder siteCoverage(float val)

Set site coverage annotation (default=Float.NaN)

allele

public net.maizegenetics.dna.map.GeneralPosition.Builder allele(WHICH_ALLELE aT,
                                                                byte val)

Set allele annotation by Allele type (default=Alignment.UNKNOWN_ALLELE)

addAnno

public net.maizegenetics.dna.map.GeneralPosition.Builder addAnno(java.lang.String key,
                                                                 java.lang.Object value)

Add non-standard annotation, boolean and String are converted to String with toString, Number are stored as Number

addAnno

public net.maizegenetics.dna.map.GeneralPosition.Builder addAnno(java.lang.String keyValue)

Add non-standard annotation with key-value separated by '='

build

public GeneralPosition build()