net.maizegenetics.dna.map

Class GenomeFeature

net.maizegenetics.dna.map.GenomeFeature

public class GenomeFeature

Created by Jason Wallace on 7/2/14. This class stores a generic "feature" on a genome, such as a gene, transcript, exon, miRNA, etc. The intent is for this information to be read in from an external file (such as an Ensembl GFF/GTF file) and collated into a GenomeFeatureMap, but it could be used in other ways.

Method Detail

id

public java.lang.String id()

type

public java.lang.String type()

parentId

public java.lang.String parentId()

chromosome

public java.lang.String chromosome()

start

public int start()

startAsString

public java.lang.String startAsString()

stop

public int stop()

stopAsString

public java.lang.String stopAsString()

getAnnotation

public java.lang.String getAnnotation(java.lang.String key)

Get any annotation based on its key. If this feature lacks that annotation, it returns 'NA'

Parameters:

key - The name of the annotation to look for

Returns:

org.jetbrains.dokka.NodeRenderContent@25264f17: The value of that annotation, or 'NA' if not found

annotations

public java.util.HashMap<java.lang.String,java.lang.String> annotations()

Returns a (shallow) copy of the Hashmap that keeps all annotations for this feature. Since the hashmap just stores Strings, a shallow copy is still safe to modify b/c it won't be reflected in the original.

Returns:

org.jetbrains.dokka.NodeRenderContent@58534b66: A copy of the Hashmap storing this feature's annotations.

toString

public java.lang.String toString()