net.maizegenetics.dna.tag

Class AbstractTags

net.maizegenetics.dna.tag.AbstractTags

All Implemented Interfaces:

Tags

Direct Known Subclasses:

AbstractTagsByTaxa, AbstractTagsHDF5, AbstractTagsOnPhysicalMap, TagCounts, TagsOnGeneticMap

public class AbstractTags
implements Tags

Basic methods for working with Tags, including sorting and search.

Field Detail

tagLengthInLong

protected int tagLengthInLong

tags

protected kotlin.Array[] tags

tagLength

protected kotlin.Array[] tagLength

Method Detail

areTagsUnique

public boolean areTagsUnique()

getTag

public kotlin.Array[] getTag(int index)

getTagCount

public int getTagCount()

getTagIndex

public int getTagIndex(kotlin.Array[] read)

getTagIndexFirst

public int getTagIndexFirst(long readFirst)

areTagsEqual

public boolean areTagsEqual(int index1,
                            int index2)

compareTags

public int compareTags(int index1,
                       int index2)

compareTags

public int compareTags(int index1,
                       kotlin.Array[] t2)

compareTags

public static int compareTags(kotlin.Array[] t1,
                              kotlin.Array[] t2)

getTagIndexSet

public kotlin.Array[] getTagIndexSet(kotlin.Array[] read)

getTagLength

public int getTagLength(int index)

getTagLength

public kotlin.Array[] getTagLength()

getTagSizeInLong

public int getTagSizeInLong()

getNullTag

public java.lang.String getNullTag()

swap

public void swap(int index1,
                 int index2)

compare

public int compare(int index1,
                   int index2)

sort

public void sort()