CombineGenotypeTable (net.maizegenetics:tassel 5.2.46 API)

java.lang.Object
- net.maizegenetics.dna.snp.CombineGenotypeTable

All Implemented Interfaces:

GenotypeTable
```
public class CombineGenotypeTable
extends Object
implements GenotypeTable
```
Combines multiple GenotypeTables together.

Author:

Terry Casstevens

Nested Class Summary
- Nested classes/interfaces inherited from interface net.maizegenetics.dna.snp.GenotypeTable
  GenotypeTable.ALLELE_SORT_TYPE, GenotypeTable.GENOTYPE_TABLE_COMPONENT

Field Summary
- Fields inherited from interface net.maizegenetics.dna.snp.GenotypeTable
  ANNOTATION_DATA_SET_DESCRIPTION, ANNOTATION_DATA_SET_NAME, GENOTYPE_TABLE_ANNOTATIONS, RARE_ALLELE, RARE_ALLELE_STR, RARE_DIPLOID_ALLELE, UNKNOWN_ALLELE, UNKNOWN_ALLELE_CHAR, UNKNOWN_ALLELE_STR, UNKNOWN_DIPLOID_ALLELE, UNKNOWN_DIPLOID_ALLELE_STR

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String[][]`	`alleleDefinitions()` Returns allele values as strings for all sites.
`String[]`	`alleleDefinitions(int site)` Same as alleleDefinitions() for only one site.
`BitSet`	`allelePresenceForAllSites(int taxon, WHICH_ALLELE allele)` Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency).
`BitSet`	`allelePresenceForAllTaxa(int site, WHICH_ALLELE allele)` Returns sequence of true/false values indicating whether site at each taxon matches a specific allele.
`long[]`	`allelePresenceForSitesBlock(int taxon, WHICH_ALLELE allele, int startBlock, int endBlock)` Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele.
`AlleleProbability`	`alleleProbability()` Returns allele probability object (null if not present)
`float`	`alleleProbability(int taxon, int site, SiteScore.SITE_SCORE_TYPE type)`
`byte[]`	`alleles(int site)` Returns all alleles at given site in order of frequency.
`byte[]`	`allelesBySortType(GenotypeTable.ALLELE_SORT_TYPE scope, int site)` Returns all alleles at given site in order defined by scope.
`int[][]`	`allelesSortedByFrequency(int site)` Return sorted list of alleles from highest frequency to lowest at given site in genotype table.
`byte`	`alternateAllele(int site)` Return (haploid) alternate allele value at given site.
`GeneralAnnotationStorage`	`annotations()` Annotations of this Genotype Table.
`BitStorage`	`bitStorage(WHICH_ALLELE allele)` Returns BitStorage for this Genotype
`int`	`chromosomalPosition(int site)` Returns the physical position at given site.
`Chromosome`	`chromosome(int site)` Return Chromosome for given site.
`Chromosome`	`chromosome(String name)` Return Chromosome with matching name.
`String`	`chromosomeName(int site)` Return Chromosome Name for given site.
`Chromosome[]`	`chromosomes()` Return all chromosomes.
`int`	`chromosomeSiteCount(Chromosome locus)` Return number of sites for given chromosome.
`int[]`	`chromosomesOffsets()` Returns starting site for each chromosome.
`GenotypeTable[]`	`compositeAlignments()` Returns individual genotype tables within this genotype table.
`AlleleDepth`	`depth()` Returns allele depth object (null if not present)
`int[]`	`depthForAlleles(int taxon, int site)` Returns depth count for each diploid allele at the given taxon and site.
`String`	`diploidAsString(int site, byte value)` Returns String representation of diploid allele value at site.
`Dosage`	`dosage()` Returns dosage object (null if not present)
`byte`	`dosage(int taxon, int site)`
`int[]`	`firstLastSiteOfChromosome(Chromosome chromosome)` Get the first (inclusive) and last (inclusive) site of the specified chromosome in this genotype table.
`Object[][]`	`genoCounts()` Returns counts of all diploid combinations from highest frequency to lowest for whole genotype table.
`String`	`genomeVersion()` Gets the Genome Assembly.
`Object[][]`	`genosSortedByFrequency(int site)` Return sorted list of diploid vales from highest frequency to lowest at given site in genotype table.
`byte`	`genotype(int taxon, Chromosome locus, int physicalPosition)` Returns diploid values for given taxon, chromosome, and physical position.
`byte`	`genotype(int taxon, int site)` Returns diploid value (genotype) for a given taxon and site.
`byte[]`	`genotypeAllSites(int taxon)` Returns sequence of diploid allele values for all sites for given taxon.
`byte[]`	`genotypeAllTaxa(int site)` Returns sequence of diploid allele values for all taxa for given site.
`byte[]`	`genotypeArray(int taxon, int site)` Returns diploid values for given taxon and site.
`String`	`genotypeAsString(int site, byte value)` Returns String representation of allele value at site.
`String`	`genotypeAsString(int taxon, int site)` Returns string representation of diploid values returned by genotype() for given taxon and site.
`String[]`	`genotypeAsStringArray(int taxon, int site)` Returns string representation of diploid values returned by genotypeArray() for given taxon and site.
`String`	`genotypeAsStringRange(int taxon, int startSite, int endSite)` Returns string representation of diploid alleles for given taxon in specified range (end site excluded).
`String`	`genotypeAsStringRow(int taxon)` Returns string representation of diploid alleles for given taxon for all sites.
`GenotypeCallTable`	`genotypeMatrix()` Returns the immutable Genotype matrix.
`byte[]`	`genotypeRange(int taxon, int startSite, int endSite)` Returns sequence of diploid allele values for given taxon in specified range (end site excluded).
`static GenotypeTable`	`getInstance(GenotypeTable[] genoTables)` This factory method combines given genoTables.
`static GenotypeTable`	`getInstance(GenotypeTable[] genoTables, boolean isUnion)` This factory method combines given genoTables.
`BitSet`	`haplotypeAllelePresenceForAllSites(int taxon, boolean firstParent, WHICH_ALLELE allele)` Returns sequence of true/false values indicating whether taxon at each site for given parent matches a specific allele.
`BitSet`	`haplotypeAllelePresenceForAllTaxa(int site, boolean firstParent, WHICH_ALLELE allele)` Returns sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency).
`long[]`	`haplotypeAllelePresenceForSitesBlock(int taxon, boolean firstParent, WHICH_ALLELE allele, int startBlock, int endBlock)` Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency).
`boolean`	`hasAlleleProbabilities()` Returns true if this genotype table has allele probabilities.
`boolean`	`hasDepth()` Returns true if this genotype table has sequencing depth.
`boolean`	`hasDosage()` Returns true if this genotype table has dosage.
`boolean`	`hasGenotype()` Returns whether this Genotype Table has Genotype values.
`boolean`	`hasReference()` Return whether this genotype table has defined reference sequence.
`boolean`	`hasReferenceProbablity()` Returns true if this genotype table has reference probability.
`boolean`	`hasSiteTranslations()`
`int`	`heterozygousCount(int site)` Returns number of heterozygous taxa at given site.
`int`	`heterozygousCountForTaxon(int taxon)` Returns number of heterozygous sites at given taxon.
`int`	`indelSize(int site)` Return size of indel at given site.
`boolean`	`isAllPolymorphic()` Returns whether all sites are polymorphic.
`boolean`	`isHeterozygous(int taxon, int site)` Returns whether allele values at given taxon and site are heterozygous.
`boolean`	`isIndel(int site)` Returns whether give site is an indel.
`boolean`	`isPhased()` Returns whether this genotype table is phased.
`boolean`	`isPolymorphic(int site)` Return whether given site is polymorphic.
`boolean`	`isPositiveStrand(int site)` Return whether is positive strand at given site.
`byte`	`majorAllele(int site)` Return most common allele at given site.
`String`	`majorAlleleAsString(int site)` Return most common allele at given site.
`int`	`majorAlleleCount(int site)` Returns the major allele count for given site.
`double`	`majorAlleleFrequency(int site)` Return frequency for major allele at given site.
`Object[][]`	`majorMinorCounts()` Returns counts of all major/minor allele combinations from highest frequency to lowest for whole genotype table.
`int`	`maxNumAlleles()` Return max number of alleles defined for any given site.
`byte`	`minorAllele(int site)` Return most common minor allele at given site.
`String`	`minorAlleleAsString(int site)` Return most common minor allele at given site.
`int`	`minorAlleleCount(int site)` Returns the minor allele count for given site.
`double`	`minorAlleleFrequency(int site)` Return frequency for most common minor allele at given site.
`byte[]`	`minorAlleles(int site)` Return all minor alleles at given site.
`int`	`numberOfSites()` Returns total number of sites of this genotype table.
`int`	`numberOfTaxa()` Returns number of taxa
`int`	`numChromosomes()` Return number of chromosomes.
`int[]`	`physicalPositions()` Returns all physical positions.
`PositionList`	`positions()` Return the position list for the genotype table.
`byte`	`referenceAllele(int site)` Return (haploid) reference allele value at given site.
`byte[]`	`referenceAlleleForAllSites()` Returns (haploid) reference alleles for all sites.
`byte[]`	`referenceAlleles(int startSite, int endSite)` Returns (haploid) reference alleles in specified range.
`ReferenceProbability`	`referenceProbability()` Returns reference probability object (null if not present)
`float`	`referenceProbability(int taxon, int site)`
`boolean`	`retainsRareAlleles()` Returns true if this genotype table retains rare alleles.
`String`	`siteName(int site)` Get SNP ID for specified site.
`int`	`siteOfPhysicalPosition(int physicalPosition, Chromosome locus)` Return site of given physical position in chromosome.
`int`	`siteOfPhysicalPosition(int physicalPosition, Chromosome locus, String snpName)` Return site of given physical position / SNP ID in chromosome.
`Set<SiteScore.SITE_SCORE_TYPE>`	`siteScoreTypes()` Return the site scores types that have value for this genotype table.
`int[]`	`siteTranslations()`
`Stream<Byte>`	`streamGenotype()`
`Stream<Byte>`	`streamGenotype(int taxon)`
`TaxaList`	`taxa()` Return taxa list of this genotype table.
`String`	`taxaName(int index)` Return taxa name at given index.
`int`	`totalGametesNonMissingForSite(int site)` Returns total number of non-missing allele values for given site.
`int`	`totalGametesNonMissingForTaxon(int taxon)` Returns total number of non-missing allele values for given taxon.
`int`	`totalNonMissingForSite(int site)` Returns total number of non-missing taxa for given site.
`int`	`totalNonMissingForTaxon(int taxon)` Returns total number of non-missing sites for given taxon.
`int`	`translateSite(int site)` Returns which genotypeTable to use.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Method Detail
  - getInstance
```
public static GenotypeTable getInstance(GenotypeTable[] genoTables)
```
    This factory method combines given genoTables. If only one genotypeTable, then it is returned unchanged. Otherwise, this requires that each genotypeTable has the same Taxa in the same order.
    
    Parameters:
    
    genoTables -
    
    Returns:
  - getInstance
```
public static GenotypeTable getInstance(GenotypeTable[] genoTables,
                                        boolean isUnion)
```
    This factory method combines given genoTables. If only one genotypeTable, then it is returned unchanged. If isUnion equals true, a union join of the Identifiers will be used to construct the combination. Any genotypeTable not containing one of the Identifiers will return unknown value for those locations. If isUnion equals false, a intersect join of the Identifiers will be used.
    
    Parameters:
    
    genoTables - genoTables to combine
    
    isUnion - whether to union or intersect join
    
    Returns:
  - genotype
```
public byte genotype(int taxon,
                     int site)
```
    Description copied from interface: GenotypeTable
    
    Returns diploid value (genotype) for a given taxon and site.
    
    Specified by:
    
    genotype in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    high four bits generally encode the more frequent allele and the lower four bits encode the less frequent allele.
  - genotypeRange
```
public byte[] genotypeRange(int taxon,
                            int startSite,
                            int endSite)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of diploid allele values for given taxon in specified range (end site excluded). Each value in array is what would be returned by genotype().
    
    Specified by:
    
    genotypeRange in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    startSite - start site
    
    endSite - end site
    
    Returns:
    
    sequence of diploid allele values.
  - genotype
```
public byte genotype(int taxon,
                     Chromosome locus,
                     int physicalPosition)
```
    Description copied from interface: GenotypeTable
    
    Returns diploid values for given taxon, chromosome, and physical position. The chromosome and physical position should map to an unique site.
    
    Specified by:
    
    genotype in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    locus - chromosome
    
    physicalPosition - physical position
    
    Returns:
    
    first four bits are the first allele value and the second four bits are the second allele value.
  - translateSite
```
public int translateSite(int site)
```
    Returns which genotypeTable to use.
    
    Parameters:
    
    site -
    
    Returns:
    
    genotypeTable index.
  - hasReference
```
public boolean hasReference()
```
    Description copied from interface: GenotypeTable
    
    Return whether this genotype table has defined reference sequence.
    
    Specified by:
    
    hasReference in interface GenotypeTable
    
    Returns:
    
    true if this genotype table has reference sequence.
  - siteName
```
public String siteName(int site)
```
    Description copied from interface: GenotypeTable
    
    Get SNP ID for specified site.
    
    Specified by:
    
    siteName in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    site name
  - numberOfSites
```
public int numberOfSites()
```
    Description copied from interface: GenotypeTable
    
    Returns total number of sites of this genotype table.
    
    Specified by:
    
    numberOfSites in interface GenotypeTable
    
    Returns:
    
    number of sites
  - chromosomeSiteCount
```
public int chromosomeSiteCount(Chromosome locus)
```
    Description copied from interface: GenotypeTable
    
    Return number of sites for given chromosome.
    
    Specified by:
    
    chromosomeSiteCount in interface GenotypeTable
    
    Parameters:
    
    locus - chromosome
    
    Returns:
    
    number of sites
  - chromosomalPosition
```
public int chromosomalPosition(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns the physical position at given site.
    
    Specified by:
    
    chromosomalPosition in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    physical position
  - siteOfPhysicalPosition
```
public int siteOfPhysicalPosition(int physicalPosition,
                                  Chromosome locus)
```
    Description copied from interface: GenotypeTable
    
    Return site of given physical position in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown.
    
    Specified by:
    
    siteOfPhysicalPosition in interface GenotypeTable
    
    Parameters:
    
    physicalPosition - physical position
    
    locus - chromosome. if null, the first chromosome is used.
    
    Returns:
    
    index
  - siteOfPhysicalPosition
```
public int siteOfPhysicalPosition(int physicalPosition,
                                  Chromosome locus,
                                  String snpName)
```
    Description copied from interface: GenotypeTable
    
    Return site of given physical position / SNP ID in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown. This is to support multiple sites with the same physical position but different SNP IDs.
    
    Specified by:
    
    siteOfPhysicalPosition in interface GenotypeTable
    
    Parameters:
    
    physicalPosition - physical position
    
    locus - chromosome. if null, the first chromosome is used.
    
    snpName - SNP ID
    
    Returns:
    
    index
  - chromosome
```
public Chromosome chromosome(int site)
```
    Description copied from interface: GenotypeTable
    
    Return Chromosome for given site.
    
    Specified by:
    
    chromosome in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    Chromosome
  - chromosomes
```
public Chromosome[] chromosomes()
```
    Description copied from interface: GenotypeTable
    
    Return all chromosomes.
    
    Specified by:
    
    chromosomes in interface GenotypeTable
    
    Returns:
    
    chromosomes
  - numChromosomes
```
public int numChromosomes()
```
    Description copied from interface: GenotypeTable
    
    Return number of chromosomes.
    
    Specified by:
    
    numChromosomes in interface GenotypeTable
    
    Returns:
    
    number of chromosomes
  - indelSize
```
public int indelSize(int site)
```
    Description copied from interface: GenotypeTable
    
    Return size of indel at given site.
    
    Specified by:
    
    indelSize in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    indel size
  - isIndel
```
public boolean isIndel(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns whether give site is an indel.
    
    Specified by:
    
    isIndel in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    true if indel
  - referenceAllele
```
public byte referenceAllele(int site)
```
    Description copied from interface: GenotypeTable
    
    Return (haploid) reference allele value at given site.
    
    Specified by:
    
    referenceAllele in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    first four bits are the encoded reference value.
  - alternateAllele
```
public byte alternateAllele(int site)
```
    Description copied from interface: GenotypeTable
    
    Return (haploid) alternate allele value at given site.
    
    Specified by:
    
    alternateAllele in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    first four bits are the encoded alternate value.
  - compositeAlignments
```
public GenotypeTable[] compositeAlignments()
```
    Description copied from interface: GenotypeTable
    
    Returns individual genotype tables within this genotype table.
    
    Specified by:
    
    compositeAlignments in interface GenotypeTable
    
    Returns:
    
    list of genotype tables.
  - majorAllele
```
public byte majorAllele(int site)
```
    Description copied from interface: GenotypeTable
    
    Return most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    majorAllele in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common allele
  - minorAllele
```
public byte minorAllele(int site)
```
    Description copied from interface: GenotypeTable
    
    Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    minorAllele in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common minor allele
  - minorAlleles
```
public byte[] minorAlleles(int site)
```
    Description copied from interface: GenotypeTable
    
    Return all minor alleles at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    minorAlleles in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    all minor alleles
  - alleles
```
public byte[] alleles(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns all alleles at given site in order of frequency. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    alleles in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    all alleles
  - minorAlleleFrequency
```
public double minorAlleleFrequency(int site)
```
    Description copied from interface: GenotypeTable
    
    Return frequency for most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    minorAlleleFrequency in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    frequency
  - allelesSortedByFrequency
```
public int[][] allelesSortedByFrequency(int site)
```
    Description copied from interface: GenotypeTable
    
    Return sorted list of alleles from highest frequency to lowest at given site in genotype table. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid values once. Higher ploids are not supported.
    
    Specified by:
    
    allelesSortedByFrequency in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    sorted list of alleles and counts
  - genotypeArray
```
public byte[] genotypeArray(int taxon,
                            int site)
```
    Description copied from interface: GenotypeTable
    
    Returns diploid values for given taxon and site. Same values as genotype(), except two values are already separated into two bytes.
    
    Specified by:
    
    genotypeArray in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    first byte (index 0) holds first allele value in right-most four bits. second byte (index 1) holds second allele value in right-most four bits.
  - genotypeAllTaxa
```
public byte[] genotypeAllTaxa(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of diploid allele values for all taxa for given site. Each value in array is what would be returned by genotype().
    
    Specified by:
    
    genotypeAllTaxa in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    sequence of diploid allele values.
  - genotypeAllSites
```
public byte[] genotypeAllSites(int taxon)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of diploid allele values for all sites for given taxon. Each value in array is what would be returned by genotype().
    
    Specified by:
    
    genotypeAllSites in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    sequence of diploid allele values.
  - allelePresenceForAllSites
```
public BitSet allelePresenceForAllSites(int taxon,
                                        WHICH_ALLELE allele)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.
    
    Specified by:
    
    allelePresenceForAllSites in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    allele - allele
    
    Returns:
    
    sequence of true/false values.
  - allelePresenceForSitesBlock
```
public long[] allelePresenceForSitesBlock(int taxon,
                                          WHICH_ALLELE allele,
                                          int startBlock,
                                          int endBlock)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele.
    
    Specified by:
    
    allelePresenceForSitesBlock in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    allele - allele
    
    startBlock - starting block
    
    endBlock - end block
    
    Returns:
    
    sequence of true/false values.
  - genotypeAsString
```
public String genotypeAsString(int taxon,
                               int site)
```
    Description copied from interface: GenotypeTable
    
    Returns string representation of diploid values returned by genotype() for given taxon and site. The default implementation separates The two allele values with a colon (:) delimiter. Nucleotide data will be represented by a single letter IUPAC code.
    
    Specified by:
    
    genotypeAsString in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    string representation of diploid values.
  - genotypeAsStringArray
```
public String[] genotypeAsStringArray(int taxon,
                                      int site)
```
    Description copied from interface: GenotypeTable
    
    Returns string representation of diploid values returned by genotypeArray() for given taxon and site. Same two allele values as genotypeAsString(), except already separated into two Strings.
    
    Specified by:
    
    genotypeAsStringArray in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    string representations of diploid values.
  - referenceAlleles
```
public byte[] referenceAlleles(int startSite,
                               int endSite)
```
    Description copied from interface: GenotypeTable
    
    Returns (haploid) reference alleles in specified range. End site not included.
    
    Specified by:
    
    referenceAlleles in interface GenotypeTable
    
    Parameters:
    
    startSite - start site
    
    endSite - end site
    
    Returns:
    
    reference allele values.
  - referenceAlleleForAllSites
```
public byte[] referenceAlleleForAllSites()
```
    Description copied from interface: GenotypeTable
    
    Returns (haploid) reference alleles for all sites.
    
    Specified by:
    
    referenceAlleleForAllSites in interface GenotypeTable
    
    Returns:
    
    reference allele values.
  - isHeterozygous
```
public boolean isHeterozygous(int taxon,
                              int site)
```
    Description copied from interface: GenotypeTable
    
    Returns whether allele values at given taxon and site are heterozygous. If two values returned by genotype() are different, this will return false.
    
    Specified by:
    
    isHeterozygous in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    whether heterozygous
  - physicalPositions
```
public int[] physicalPositions()
```
    Description copied from interface: GenotypeTable
    
    Returns all physical positions.
    
    Specified by:
    
    physicalPositions in interface GenotypeTable
    
    Returns:
    
    physical positions.
  - chromosomeName
```
public String chromosomeName(int site)
```
    Description copied from interface: GenotypeTable
    
    Return Chromosome Name for given site.
    
    Specified by:
    
    chromosomeName in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    Chromosome Name
  - chromosomesOffsets
```
public int[] chromosomesOffsets()
```
    Description copied from interface: GenotypeTable
    
    Returns starting site for each chromosome.
    
    Specified by:
    
    chromosomesOffsets in interface GenotypeTable
    
    Returns:
    
    starting site for each chromosome.
  - siteScoreTypes
```
public Set<SiteScore.SITE_SCORE_TYPE> siteScoreTypes()
```
    Description copied from interface: GenotypeTable
    
    Return the site scores types that have value for this genotype table.
    
    Specified by:
    
    siteScoreTypes in interface GenotypeTable
    
    Returns:
    
    site score types.
  - isAllPolymorphic
```
public boolean isAllPolymorphic()
```
    Description copied from interface: GenotypeTable
    
    Returns whether all sites are polymorphic.
    
    Specified by:
    
    isAllPolymorphic in interface GenotypeTable
    
    Returns:
    
    true if all sites are polymorphic.
  - isPolymorphic
```
public boolean isPolymorphic(int site)
```
    Description copied from interface: GenotypeTable
    
    Return whether given site is polymorphic.
    
    Specified by:
    
    isPolymorphic in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    true if given site is polymorphic.
  - majorAlleleFrequency
```
public double majorAlleleFrequency(int site)
```
    Description copied from interface: GenotypeTable
    
    Return frequency for major allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    majorAlleleFrequency in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    frequency
  - genomeVersion
```
public String genomeVersion()
```
    Description copied from interface: GenotypeTable
    
    Gets the Genome Assembly.
    
    Specified by:
    
    genomeVersion in interface GenotypeTable
    
    Returns:
    
    the genome assembly.
  - isPositiveStrand
```
public boolean isPositiveStrand(int site)
```
    Description copied from interface: GenotypeTable
    
    Return whether is positive strand at given site.
    
    Specified by:
    
    isPositiveStrand in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    whether is positive strand.
  - isPhased
```
public boolean isPhased()
```
    Description copied from interface: GenotypeTable
    
    Returns whether this genotype table is phased.
    
    Specified by:
    
    isPhased in interface GenotypeTable
    
    Returns:
    
    true if phased.
  - retainsRareAlleles
```
public boolean retainsRareAlleles()
```
    Description copied from interface: GenotypeTable
    
    Returns true if this genotype table retains rare alleles. If false, rare alleles are recorded as unknown.
    
    Specified by:
    
    retainsRareAlleles in interface GenotypeTable
    
    Returns:
    
    whether rare alleles are retained.
  - alleleDefinitions
```
public String[][] alleleDefinitions()
```
    Description copied from interface: GenotypeTable
    
    Returns allele values as strings for all sites. The first dimension of the array indexes the sites. The second dimension indexes the allele values for given site. The indices for the allele values are used as the codes to store data. These codes (indices) are returned by the genotype() methods. If only one array of allele values is returned, that is the encoding for all sites.
    
    Specified by:
    
    alleleDefinitions in interface GenotypeTable
    
    Returns:
    
    allele values for all sites.
  - alleleDefinitions
```
public String[] alleleDefinitions(int site)
```
    Description copied from interface: GenotypeTable
    
    Same as alleleDefinitions() for only one site.
    
    Specified by:
    
    alleleDefinitions in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    allele values for given site.
  - genotypeAsString
```
public String genotypeAsString(int site,
                               byte value)
```
    Description copied from interface: GenotypeTable
    
    Returns String representation of allele value at site.
    
    Specified by:
    
    genotypeAsString in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    value - allele value
    
    Returns:
    
    String representation
  - maxNumAlleles
```
public int maxNumAlleles()
```
    Description copied from interface: GenotypeTable
    
    Return max number of alleles defined for any given site.
    
    Specified by:
    
    maxNumAlleles in interface GenotypeTable
    
    Returns:
    
    max number of alleles.
  - totalGametesNonMissingForSite
```
public int totalGametesNonMissingForSite(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns total number of non-missing allele values for given site. This can be twice the number of taxa, as diploid values are supported.
    
    Specified by:
    
    totalGametesNonMissingForSite in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    number of non-missing allele values.
  - heterozygousCount
```
public int heterozygousCount(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns number of heterozygous taxa at given site.
    
    Specified by:
    
    heterozygousCount in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    number of heterozygous taxa
  - minorAlleleCount
```
public int minorAlleleCount(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns the minor allele count for given site.
    
    Specified by:
    
    minorAlleleCount in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    minor allele count
  - majorAlleleCount
```
public int majorAlleleCount(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns the major allele count for given site.
    
    Specified by:
    
    majorAlleleCount in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    major allele count
  - genosSortedByFrequency
```
public Object[][] genosSortedByFrequency(int site)
```
    Description copied from interface: GenotypeTable
    
    Return sorted list of diploid vales from highest frequency to lowest at given site in genotype table. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Integers).
    
    Specified by:
    
    genosSortedByFrequency in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    sorted list of diploids and counts
  - allelesBySortType
```
public byte[] allelesBySortType(GenotypeTable.ALLELE_SORT_TYPE scope,
                                int site)
```
    Description copied from interface: GenotypeTable
    
    Returns all alleles at given site in order defined by scope.
    
    Specified by:
    
    allelesBySortType in interface GenotypeTable
    
    Parameters:
    
    scope - scope
    
    site - site
    
    Returns:
    
    alleles
  - allelePresenceForAllTaxa
```
public BitSet allelePresenceForAllTaxa(int site,
                                       WHICH_ALLELE allele)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of true/false values indicating whether site at each taxon matches a specific allele.
    
    Specified by:
    
    allelePresenceForAllTaxa in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    allele - allele
    
    Returns:
    
    sequence of true/false values.
  - haplotypeAllelePresenceForAllSites
```
public BitSet haplotypeAllelePresenceForAllSites(int taxon,
                                                 boolean firstParent,
                                                 WHICH_ALLELE allele)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of true/false values indicating whether taxon at each site for given parent matches a specific allele.
    
    Specified by:
    
    haplotypeAllelePresenceForAllSites in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    firstParent - true for first parent (false for second parent)
    
    allele - allele
    
    Returns:
    
    sequence of true/false values.
  - haplotypeAllelePresenceForAllTaxa
```
public BitSet haplotypeAllelePresenceForAllTaxa(int site,
                                                boolean firstParent,
                                                WHICH_ALLELE allele)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of true/false values indicating whether site at each taxon for given parent matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.
    
    Specified by:
    
    haplotypeAllelePresenceForAllTaxa in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    firstParent - true for first parent (false for second parent)
    
    allele - allele
    
    Returns:
    
    sequence of true/false values.
  - haplotypeAllelePresenceForSitesBlock
```
public long[] haplotypeAllelePresenceForSitesBlock(int taxon,
                                                   boolean firstParent,
                                                   WHICH_ALLELE allele,
                                                   int startBlock,
                                                   int endBlock)
```
    Description copied from interface: GenotypeTable
    
    Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) for given parent matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.
    
    Specified by:
    
    haplotypeAllelePresenceForSitesBlock in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    firstParent - true for first parent (false for second parent)
    
    allele - allele
    
    startBlock - starting block
    
    endBlock - end block
    
    Returns:
    
    sequence of true/false values.
  - genotypeAsStringRange
```
public String genotypeAsStringRange(int taxon,
                                    int startSite,
                                    int endSite)
```
    Description copied from interface: GenotypeTable
    
    Returns string representation of diploid alleles for given taxon in specified range (end site excluded). Each value in string is what would be returned by genotypeAsString().
    
    Specified by:
    
    genotypeAsStringRange in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    startSite - start site
    
    endSite - end site
    
    Returns:
    
    string representation of alleles in range
  - genotypeAsStringRow
```
public String genotypeAsStringRow(int taxon)
```
    Description copied from interface: GenotypeTable
    
    Returns string representation of diploid alleles for given taxon for all sites. Each value in string is what would be returned by genotypeAsString().
    
    Specified by:
    
    genotypeAsStringRow in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    string representation of alleles
  - firstLastSiteOfChromosome
```
public int[] firstLastSiteOfChromosome(Chromosome chromosome)
```
    Description copied from interface: GenotypeTable
    
    Get the first (inclusive) and last (inclusive) site of the specified chromosome in this genotype table.
    
    Specified by:
    
    firstLastSiteOfChromosome in interface GenotypeTable
    
    Parameters:
    
    chromosome - chromosome
    
    Returns:
    
    first and last site
  - numberOfTaxa
```
public int numberOfTaxa()
```
    Description copied from interface: GenotypeTable
    
    Returns number of taxa
    
    Specified by:
    
    numberOfTaxa in interface GenotypeTable
    
    Returns:
    
    number of taxa
  - chromosome
```
public Chromosome chromosome(String name)
```
    Description copied from interface: GenotypeTable
    
    Return Chromosome with matching name. First to match will be returned.
    
    Specified by:
    
    chromosome in interface GenotypeTable
    
    Parameters:
    
    name - name
    
    Returns:
    
    Chromosome
  - majorAlleleAsString
```
public String majorAlleleAsString(int site)
```
    Description copied from interface: GenotypeTable
    
    Return most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    majorAlleleAsString in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common allele as String
  - minorAlleleAsString
```
public String minorAlleleAsString(int site)
```
    Description copied from interface: GenotypeTable
    
    Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    minorAlleleAsString in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common minor allele as String
  - taxa
```
public TaxaList taxa()
```
    Description copied from interface: GenotypeTable
    
    Return taxa list of this genotype table.
    
    Specified by:
    
    taxa in interface GenotypeTable
    
    Returns:
    
    taxa list.
  - taxaName
```
public String taxaName(int index)
```
    Description copied from interface: GenotypeTable
    
    Return taxa name at given index.
    
    Specified by:
    
    taxaName in interface GenotypeTable
    
    Returns:
    
    taxa name
  - diploidAsString
```
public String diploidAsString(int site,
                              byte value)
```
    Description copied from interface: GenotypeTable
    
    Returns String representation of diploid allele value at site.
    
    Specified by:
    
    diploidAsString in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    value - diploid allele value
    
    Returns:
    
    String representation
  - totalNonMissingForSite
```
public int totalNonMissingForSite(int site)
```
    Description copied from interface: GenotypeTable
    
    Returns total number of non-missing taxa for given site. Taxa are considered missing only if both allele values are Unknown (N).
    
    Specified by:
    
    totalNonMissingForSite in interface GenotypeTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    number of non-missing taxa..
  - genoCounts
```
public Object[][] genoCounts()
```
    Description copied from interface: GenotypeTable
    
    Returns counts of all diploid combinations from highest frequency to lowest for whole genotype table. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Longs).
    
    Specified by:
    
    genoCounts in interface GenotypeTable
    
    Returns:
    
    diploid counts.
  - majorMinorCounts
```
public Object[][] majorMinorCounts()
```
    Description copied from interface: GenotypeTable
    
    Returns counts of all major/minor allele combinations from highest frequency to lowest for whole genotype table. Resulting double dimension array holds major/minor allele (Strings) in result[0]. And the counts are in result[1] (Longs).
    
    Specified by:
    
    majorMinorCounts in interface GenotypeTable
    
    Returns:
    
    diploid counts.
  - totalGametesNonMissingForTaxon
```
public int totalGametesNonMissingForTaxon(int taxon)
```
    Description copied from interface: GenotypeTable
    
    Returns total number of non-missing allele values for given taxon. This can be twice the number of sites, as diploid values are supported.
    
    Specified by:
    
    totalGametesNonMissingForTaxon in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    number of non-missing allele values.
  - heterozygousCountForTaxon
```
public int heterozygousCountForTaxon(int taxon)
```
    Description copied from interface: GenotypeTable
    
    Returns number of heterozygous sites at given taxon.
    
    Specified by:
    
    heterozygousCountForTaxon in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    number of heterozygous sites
  - totalNonMissingForTaxon
```
public int totalNonMissingForTaxon(int taxon)
```
    Description copied from interface: GenotypeTable
    
    Returns total number of non-missing sites for given taxon. Sites are considered missing only if both allele values are Unknown (N).
    
    Specified by:
    
    totalNonMissingForTaxon in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    number of non-missing sites.
  - hasGenotype
```
public boolean hasGenotype()
```
    Description copied from interface: GenotypeTable
    
    Returns whether this Genotype Table has Genotype values.
    
    Specified by:
    
    hasGenotype in interface GenotypeTable
    
    Returns:
    
    has genotype values.
  - hasDepth
```
public boolean hasDepth()
```
    Description copied from interface: GenotypeTable
    
    Returns true if this genotype table has sequencing depth.
    
    Specified by:
    
    hasDepth in interface GenotypeTable
    
    Returns:
    
    true if this genotype table has sequencing depth.
  - hasAlleleProbabilities
```
public boolean hasAlleleProbabilities()
```
    Description copied from interface: GenotypeTable
    
    Returns true if this genotype table has allele probabilities.
    
    Specified by:
    
    hasAlleleProbabilities in interface GenotypeTable
    
    Returns:
    
    true if this genotype table has allele probabilities.
  - hasReferenceProbablity
```
public boolean hasReferenceProbablity()
```
    Description copied from interface: GenotypeTable
    
    Returns true if this genotype table has reference probability.
    
    Specified by:
    
    hasReferenceProbablity in interface GenotypeTable
    
    Returns:
    
    true if this genotype table has reference probability.
  - hasDosage
```
public boolean hasDosage()
```
    Description copied from interface: GenotypeTable
    
    Returns true if this genotype table has dosage.
    
    Specified by:
    
    hasDosage in interface GenotypeTable
    
    Returns:
    
    true if this genotype table has dosage.
  - depth
```
public AlleleDepth depth()
```
    Description copied from interface: GenotypeTable
    
    Returns allele depth object (null if not present)
    
    Specified by:
    
    depth in interface GenotypeTable
    
    Returns:
    
    allele depth associated with genotypeTable
  - depthForAlleles
```
public int[] depthForAlleles(int taxon,
                             int site)
```
    Description copied from interface: GenotypeTable
    
    Returns depth count for each diploid allele at the given taxon and site.
    
    Specified by:
    
    depthForAlleles in interface GenotypeTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    two counts
  - bitStorage
```
public BitStorage bitStorage(WHICH_ALLELE allele)
```
    Description copied from interface: GenotypeTable
    
    Returns BitStorage for this Genotype
    
    Specified by:
    
    bitStorage in interface GenotypeTable
    
    Parameters:
    
    allele - allele
    
    Returns:
    
    BitStorage
  - positions
```
public PositionList positions()
```
    Description copied from interface: GenotypeTable
    
    Return the position list for the genotype table.
    
    Specified by:
    
    positions in interface GenotypeTable
    
    Returns:
    
    PositionList for all sites.
  - genotypeMatrix
```
public GenotypeCallTable genotypeMatrix()
```
    Description copied from interface: GenotypeTable
    
    Returns the immutable Genotype matrix. Taxa and Positions are not part of the matrix. This method is used for copying Genotype tables, when either the Taxa or Positions have changed.
    
    Specified by:
    
    genotypeMatrix in interface GenotypeTable
    
    Returns:
    
    genotype matrix
  - alleleProbability
```
public AlleleProbability alleleProbability()
```
    Description copied from interface: GenotypeTable
    
    Returns allele probability object (null if not present)
    
    Specified by:
    
    alleleProbability in interface GenotypeTable
    
    Returns:
    
    allele probability associated with genotypeTable
  - alleleProbability
```
public float alleleProbability(int taxon,
                               int site,
                               SiteScore.SITE_SCORE_TYPE type)
```
    Specified by:
    
    alleleProbability in interface GenotypeTable
  - referenceProbability
```
public ReferenceProbability referenceProbability()
```
    Description copied from interface: GenotypeTable
    
    Returns reference probability object (null if not present)
    
    Specified by:
    
    referenceProbability in interface GenotypeTable
    
    Returns:
    
    reference probability associated with genotypeTable
  - referenceProbability
```
public float referenceProbability(int taxon,
                                  int site)
```
    Specified by:
    
    referenceProbability in interface GenotypeTable
  - dosage
```
public Dosage dosage()
```
    Description copied from interface: GenotypeTable
    
    Returns dosage object (null if not present)
    
    Specified by:
    
    dosage in interface GenotypeTable
    
    Returns:
    
    dosage associated with genotypeTable
  - dosage
```
public byte dosage(int taxon,
                   int site)
```
    Specified by:
    
    dosage in interface GenotypeTable
  - annotations
```
public GeneralAnnotationStorage annotations()
```
    Description copied from interface: GenotypeTable
    
    Annotations of this Genotype Table. Null if there are none.
    
    Specified by:
    
    annotations in interface GenotypeTable
    
    Returns:
    
    Annotations or null
  - streamGenotype
```
public Stream<Byte> streamGenotype()
```
    Specified by:
    
    streamGenotype in interface GenotypeTable
  - streamGenotype
```
public Stream<Byte> streamGenotype(int taxon)
```
    Specified by:
    
    streamGenotype in interface GenotypeTable
  - hasSiteTranslations
```
public boolean hasSiteTranslations()
```
    Specified by:
    
    hasSiteTranslations in interface GenotypeTable
  - siteTranslations
```
public int[] siteTranslations()
```
    Specified by:
    
    siteTranslations in interface GenotypeTable

Class CombineGenotypeTable

Nested Class Summary

Nested classes/interfaces inherited from interface net.maizegenetics.dna.snp.GenotypeTable

Field Summary

Fields inherited from interface net.maizegenetics.dna.snp.GenotypeTable

Method Summary

Methods inherited from class java.lang.Object

Method Detail

getInstance

getInstance

genotype

genotypeRange

genotype

translateSite

hasReference

siteName

numberOfSites

chromosomeSiteCount

chromosomalPosition

siteOfPhysicalPosition

siteOfPhysicalPosition

chromosome

chromosomes

numChromosomes

indelSize

isIndel

referenceAllele

alternateAllele

compositeAlignments

majorAllele

minorAllele

minorAlleles

alleles

minorAlleleFrequency

allelesSortedByFrequency

genotypeArray

genotypeAllTaxa

genotypeAllSites

allelePresenceForAllSites

allelePresenceForSitesBlock

genotypeAsString

genotypeAsStringArray

referenceAlleles

referenceAlleleForAllSites

isHeterozygous

physicalPositions

chromosomeName

chromosomesOffsets

siteScoreTypes

isAllPolymorphic

isPolymorphic

majorAlleleFrequency

genomeVersion

isPositiveStrand

isPhased

retainsRareAlleles

alleleDefinitions

alleleDefinitions

genotypeAsString

maxNumAlleles

totalGametesNonMissingForSite

heterozygousCount

minorAlleleCount

majorAlleleCount

genosSortedByFrequency

allelesBySortType

allelePresenceForAllTaxa

haplotypeAllelePresenceForAllSites

haplotypeAllelePresenceForAllTaxa

haplotypeAllelePresenceForSitesBlock

genotypeAsStringRange

genotypeAsStringRow

firstLastSiteOfChromosome

numberOfTaxa

chromosome

majorAlleleAsString

minorAlleleAsString

taxa

taxaName

diploidAsString