net.maizegenetics.dna.tag

Class AbstractTag

net.maizegenetics.dna.tag.AbstractTag

All Implemented Interfaces:

Tag

public class AbstractTag
implements Tag

Created by edbuckler on 7/26/14.

Constructor Detail

AbstractTag

protected AbstractTag(short length,
                      boolean reference,
                      java.lang.String name)

Method Detail

seqLength

public short seqLength()

isReference

public boolean isReference()

name

public java.lang.String name()

sequence

public java.lang.String sequence()

seq2BitAsBytes

public kotlin.Array[] seq2BitAsBytes()

compareTo

public int compareTo(Tag o)

equals

public boolean equals(java.lang.Object o)

hashCode

public int hashCode()

toString

public java.lang.String toString()

getSequenceFromLong

protected static java.lang.String getSequenceFromLong(kotlin.Array[] val,
                                                      int length)

Return a string representation of an array of 2-bit encoded longs.

Parameters:

val - array of 2-bit encoded sequences

Returns:

org.jetbrains.dokka.NodeRenderContent@39ad1b81: DNA sequence as a string

getLongArrayFromSeq

protected static kotlin.Array[] getLongArrayFromSeq(java.lang.String seq)

Parameters:

seq - A String containing a DNA sequence.

Returns:

org.jetbrains.dokka.NodeRenderContent@2d319df8: result A array of Long containing the binary representation of the sequence. null if sequence length has any non-DNA characters