net.maizegenetics.dna.factor.FeatureTable.kt Maven / Gradle / Ivy

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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.

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package net.maizegenetics.dna.factor

import net.maizegenetics.dna.factor.site.FeatureSite
import net.maizegenetics.taxa.TaxaList

/**
 * @author Terry Casstevens
 * Created November 13, 2018
 */

const val UNKNOWN_ALLELE = 0xFF.toByte()
const val UNKNOWN_ALLELE_STR = "N"

class FeatureTable(val taxa: TaxaList, private var sites: List) : List by sites {

    init {
        sites = sites.sorted()
    }

    fun numTaxa() = taxa.size

    fun numFeatures() = sites.size

    fun taxa() = taxa

    fun site(index: Int): FeatureSite = sites[index]

}