LineIndexHapmapGenotypeCallTable (net.maizegenetics:tassel 5.2.46 API)

java.lang.Object
- net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable

All Implemented Interfaces:

GenotypeCallTable
```
public class LineIndexHapmapGenotypeCallTable
extends Object
```
Author:

Terry Casstevens

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 getAlleleEncodings() for only one site.
`byte[]`	`alleles(int site)` Returns all alleles at given site in order of frequency.
`int[][]`	`allelesSortedByFrequency(int site)` Return sorted list of alleles from highest frequency to lowest at given site in alignment.
`String`	`diploidAsString(int site, byte value)` Returns String representation of diploid allele value at site.
`Object[][]`	`genoCounts()` Returns counts of all diploid combinations from highest frequency to lowest for whole alignment.
`Object[][]`	`genosSortedByFrequency(int site)` Return sorted list of diploid vales from highest frequency to lowest at given site in alignment.
`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[]`	`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 site, byte value)` Same as genotypeAsStringArray(taxon, site), except given value is converted for given 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.
`byte[]`	`genotypeForAllSites(int taxon)` Get all genotypes for given taxon.
`byte[]`	`genotypeForAllTaxa(int site)` Get all genotypes for given site.
`byte[]`	`genotypeForSiteRange(int taxon, int start, int end)` Get all genotypes for given taxon from start site (inclusive) to end site (exclusive).
`byte[]`	`genotypeRange(int taxon, int startSite, int endSite)` Returns sequence of diploid allele values for given taxon in specified range (end site excluded).
`static LineIndexHapmapGenotypeCallTable`	`getInstance(int numTaxa, int numSites, boolean phased, boolean isOneLetter, LineIndex index, String filename)`
`int`	`heterozygousCount(int site)` Returns number of heterozygous taxa at given site.
`int`	`heterozygousCountForTaxon(int taxon)` Returns number of heterozygous sites at given taxon.
`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`	`isPhased()` Returns whether this alignment is phased.
`boolean`	`isPolymorphic(int site)` Return whether given site is polymorphic.
`boolean`	`isSiteOptimized()` This returns true if this Genotype performs better when processing whole sites at a time.
`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.
`byte[]`	`majorAlleleForAllSites()` Returns major allele for all sites.
`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 alignment.
`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.
`byte[]`	`minorAlleleForAllSites()` Returns minor allele for all sites.
`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 in this genotype.
`int`	`numberOfTaxa()` Returns number of taxa (samples) in this genotype
`boolean`	`retainsRareAlleles()` Returns true if this Alignment retains rare alleles.
`Stats`	`siteStats(int site)`
`Spliterator<Byte>`	`spliterator()`
`Stream<Byte>`	`stream()` Returns a Stream over the genotype calls.
`Stream<Byte>`	`stream(int taxon)`
`Stats`	`taxonStats(int taxon)`
`byte`	`thirdAllele(int site)` Return the second minor allele at given site (Third allele state).
`byte[]`	`thirdAlleleForAllSites()` Returns third (second minor) allele for all sites.
`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.
`void`	`transposeData(boolean siteInnerLoop)` Tells this Genotype to transpose it's data to optimize performance for given iteration nesting.

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

- Method Detail
  - getInstance
```
public static LineIndexHapmapGenotypeCallTable getInstance(int numTaxa,
                                                           int numSites,
                                                           boolean phased,
                                                           boolean isOneLetter,
                                                           LineIndex index,
                                                           String filename)
```
  - genotype
```
public byte genotype(int taxon,
                     int site)
```
    Description copied from interface: GenotypeCallTable
    
    Returns diploid value (genotype) for a given taxon and site.
    
    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.
  - genotypeForAllTaxa
```
public byte[] genotypeForAllTaxa(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Get all genotypes for given site.
    
    Specified by:
    
    genotypeForAllTaxa in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    genotypes
  - genotypeAsString
```
public String genotypeAsString(int taxon,
                               int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    string representation of diploid values.
  - diploidAsString
```
public String diploidAsString(int site,
                              byte value)
```
    Description copied from interface: GenotypeCallTable
    
    Returns String representation of diploid allele value at site.
    
    Specified by:
    
    diploidAsString in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    value - diploid allele value
    
    Returns:
    
    String representation
  - transposeData
```
public void transposeData(boolean siteInnerLoop)
```
    Description copied from interface: GenotypeCallTable
    
    Tells this Genotype to transpose it's data to optimize performance for given iteration nesting. If siteInnerLoop is true, performance better when looping through sites inside taxa loop. If false, performance better when looping through taxa inside site loop.
    
    Parameters:
    
    siteInnerLoop - flag for which iteration
  - isSiteOptimized
```
public boolean isSiteOptimized()
```
    Description copied from interface: GenotypeCallTable
    
    This returns true if this Genotype performs better when processing whole sites at a time. Return false if performance is better when processing whole taxa.
    
    Returns:
    
    true if optimized for site processing
  - genotypeArray
```
public byte[] genotypeArray(int taxon,
                            int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    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.
  - genotypeRange
```
public byte[] genotypeRange(int taxon,
                            int startSite,
                            int endSite)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    startSite - start site
    
    endSite - end site
    
    Returns:
    
    sequence of diploid allele values.
  - genotypeAllSites
```
public byte[] genotypeAllSites(int taxon)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    sequence of diploid allele values.
  - genotypeAsStringRange
```
public String genotypeAsStringRange(int taxon,
                                    int startSite,
                                    int endSite)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    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: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    string representation of alleles
  - genotypeAsStringArray
```
public String[] genotypeAsStringArray(int taxon,
                                      int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    string representations of diploid values.
  - genotypeAsStringArray
```
public String[] genotypeAsStringArray(int site,
                                      byte value)
```
    Description copied from interface: GenotypeCallTable
    
    Same as genotypeAsStringArray(taxon, site), except given value is converted for given site.
    
    Specified by:
    
    genotypeAsStringArray in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    value - diploid allele value
    
    Returns:
    
    String representation
  - allelesSortedByFrequency
```
public int[][] allelesSortedByFrequency(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Return sorted list of alleles from highest frequency to lowest at given site in alignment. 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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    sorted list of alleles and counts
  - isHeterozygous
```
public boolean isHeterozygous(int taxon,
                              int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    site - site
    
    Returns:
    
    whether heterozygous
  - heterozygousCount
```
public int heterozygousCount(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Returns number of heterozygous taxa at given site.
    
    Specified by:
    
    heterozygousCount in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    number of heterozygous taxa
  - isPolymorphic
```
public boolean isPolymorphic(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Return whether given site is polymorphic.
    
    Specified by:
    
    isPolymorphic in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    true if given site is polymorphic.
  - isAllPolymorphic
```
public boolean isAllPolymorphic()
```
    Description copied from interface: GenotypeCallTable
    
    Returns whether all sites are polymorphic.
    
    Specified by:
    
    isAllPolymorphic in interface GenotypeCallTable
    
    Returns:
    
    true if all sites are polymorphic.
  - isPhased
```
public boolean isPhased()
```
    Description copied from interface: GenotypeCallTable
    
    Returns whether this alignment is phased.
    
    Specified by:
    
    isPhased in interface GenotypeCallTable
    
    Returns:
    
    true if phased.
  - retainsRareAlleles
```
public boolean retainsRareAlleles()
```
    Description copied from interface: GenotypeCallTable
    
    Returns true if this Alignment retains rare alleles. If false, rare alleles are recorded as unknown.
    
    Specified by:
    
    retainsRareAlleles in interface GenotypeCallTable
    
    Returns:
    
    whether rare alleles are retained.
  - alleleDefinitions
```
public String[][] alleleDefinitions()
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Returns:
    
    allele values for all sites.
  - alleleDefinitions
```
public String[] alleleDefinitions(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Same as getAlleleEncodings() for only one site.
    
    Specified by:
    
    alleleDefinitions in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    allele values for given site.
  - genotypeAsString
```
public String genotypeAsString(int site,
                               byte value)
```
    Description copied from interface: GenotypeCallTable
    
    Returns String representation of allele value at site.
    
    Specified by:
    
    genotypeAsString in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    value - allele value
    
    Returns:
    
    String representation
  - maxNumAlleles
```
public int maxNumAlleles()
```
    Description copied from interface: GenotypeCallTable
    
    Return max number of alleles defined for any given site.
    
    Specified by:
    
    maxNumAlleles in interface GenotypeCallTable
    
    Returns:
    
    max number of alleles.
  - totalGametesNonMissingForSite
```
public int totalGametesNonMissingForSite(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    number of non-missing allele values.
  - totalNonMissingForSite
```
public int totalNonMissingForSite(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    number of non-missing taxa..
  - majorAlleleForAllSites
```
public byte[] majorAlleleForAllSites()
```
    Description copied from interface: GenotypeCallTable
    
    Returns major allele for all sites.
    
    Specified by:
    
    majorAlleleForAllSites in interface GenotypeCallTable
    
    Returns:
    
    all major alleles
  - minorAlleleForAllSites
```
public byte[] minorAlleleForAllSites()
```
    Description copied from interface: GenotypeCallTable
    
    Returns minor allele for all sites.
    
    Specified by:
    
    minorAlleleForAllSites in interface GenotypeCallTable
    
    Returns:
    
    all minor alleles
  - thirdAlleleForAllSites
```
public byte[] thirdAlleleForAllSites()
```
    Description copied from interface: GenotypeCallTable
    
    Returns third (second minor) allele for all sites.
    
    Specified by:
    
    thirdAlleleForAllSites in interface GenotypeCallTable
    
    Returns:
    
    all third alleles
  - thirdAllele
```
public byte thirdAllele(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Return the second minor allele at given site (Third allele state). Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
    
    Specified by:
    
    thirdAllele in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    second minor allele
  - minorAlleleCount
```
public int minorAlleleCount(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Returns the minor allele count for given site.
    
    Specified by:
    
    minorAlleleCount in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    minor allele count
  - minorAllele
```
public byte minorAllele(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common minor allele
  - minorAlleleAsString
```
public String minorAlleleAsString(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common minor allele as String
  - minorAlleles
```
public byte[] minorAlleles(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    all minor alleles
  - majorAlleleCount
```
public int majorAlleleCount(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Returns the major allele count for given site.
    
    Specified by:
    
    majorAlleleCount in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    major allele count
  - majorAllele
```
public byte majorAllele(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common allele
  - majorAlleleAsString
```
public String majorAlleleAsString(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    most common allele as String
  - majorAlleleFrequency
```
public double majorAlleleFrequency(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    frequency
  - minorAlleleFrequency
```
public double minorAlleleFrequency(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    frequency
  - genosSortedByFrequency
```
public Object[][] genosSortedByFrequency(int site)
```
    Description copied from interface: GenotypeCallTable
    
    Return sorted list of diploid vales from highest frequency to lowest at given site in alignment. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Integers).
    
    Specified by:
    
    genosSortedByFrequency in interface GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    sorted list of diploids and counts
  - genoCounts
```
public Object[][] genoCounts()
```
    Description copied from interface: GenotypeCallTable
    
    Returns counts of all diploid combinations from highest frequency to lowest for whole alignment. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Longs).
    
    Specified by:
    
    genoCounts in interface GenotypeCallTable
    
    Returns:
    
    diploid counts.
  - majorMinorCounts
```
public Object[][] majorMinorCounts()
```
    Description copied from interface: GenotypeCallTable
    
    Returns counts of all major/minor allele combinations from highest frequency to lowest for whole alignment. 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 GenotypeCallTable
    
    Returns:
    
    diploid counts.
  - totalGametesNonMissingForTaxon
```
public int totalGametesNonMissingForTaxon(int taxon)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    number of non-missing allele values.
  - heterozygousCountForTaxon
```
public int heterozygousCountForTaxon(int taxon)
```
    Description copied from interface: GenotypeCallTable
    
    Returns number of heterozygous sites at given taxon.
    
    Specified by:
    
    heterozygousCountForTaxon in interface GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    number of heterozygous sites
  - totalNonMissingForTaxon
```
public int totalNonMissingForTaxon(int taxon)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    number of non-missing sites.
  - alleles
```
public byte[] alleles(int site)
```
    Description copied from interface: GenotypeCallTable
    
    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 GenotypeCallTable
    
    Parameters:
    
    site - site
    
    Returns:
    
    all alleles
  - numberOfSites
```
public int numberOfSites()
```
    Description copied from interface: GenotypeCallTable
    
    Returns total number of sites in this genotype.
    
    Specified by:
    
    numberOfSites in interface GenotypeCallTable
    
    Returns:
    
    number of sites
  - numberOfTaxa
```
public int numberOfTaxa()
```
    Description copied from interface: GenotypeCallTable
    
    Returns number of taxa (samples) in this genotype
    
    Specified by:
    
    numberOfTaxa in interface GenotypeCallTable
    
    Returns:
    
    number of taxa
  - genotypeForAllSites
```
public byte[] genotypeForAllSites(int taxon)
```
    Description copied from interface: GenotypeCallTable
    
    Get all genotypes for given taxon.
    
    Specified by:
    
    genotypeForAllSites in interface GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    genotypes
  - genotypeForSiteRange
```
public byte[] genotypeForSiteRange(int taxon,
                                   int start,
                                   int end)
```
    Description copied from interface: GenotypeCallTable
    
    Get all genotypes for given taxon from start site (inclusive) to end site (exclusive).
    
    Specified by:
    
    genotypeForSiteRange in interface GenotypeCallTable
    
    Parameters:
    
    taxon - taxon
    
    start - start
    
    end - end
    
    Returns:
    
    genotypes
  - siteStats
```
public Stats siteStats(int site)
```
    Specified by:
    
    siteStats in interface GenotypeCallTable
  - taxonStats
```
public Stats taxonStats(int taxon)
```
    Specified by:
    
    taxonStats in interface GenotypeCallTable
  - stream
```
public Stream<Byte> stream()
```
    Description copied from interface: GenotypeCallTable
    
    Returns a Stream over the genotype calls.
    
    Specified by:
    
    stream in interface GenotypeCallTable
    
    Returns:
    
    Stream over the genotype calls
  - stream
```
public Stream<Byte> stream(int taxon)
```
    Specified by:
    
    stream in interface GenotypeCallTable
  - spliterator
```
public Spliterator<Byte> spliterator()
```

Class LineIndexHapmapGenotypeCallTable

Method Summary

Methods inherited from class java.lang.Object

Method Detail

getInstance

genotype

genotypeForAllTaxa

genotypeAsString

diploidAsString

transposeData

isSiteOptimized

genotypeArray

genotypeRange

genotypeAllSites

genotypeAsStringRange

genotypeAsStringRow

genotypeAsStringArray

genotypeAsStringArray

allelesSortedByFrequency

isHeterozygous

heterozygousCount

isPolymorphic

isAllPolymorphic

isPhased

retainsRareAlleles

alleleDefinitions

alleleDefinitions

genotypeAsString

maxNumAlleles

totalGametesNonMissingForSite

totalNonMissingForSite

majorAlleleForAllSites

minorAlleleForAllSites

thirdAlleleForAllSites

thirdAllele

minorAlleleCount

minorAllele

minorAlleleAsString

minorAlleles

majorAlleleCount

majorAllele

majorAlleleAsString

majorAlleleFrequency

minorAlleleFrequency

genosSortedByFrequency

genoCounts

majorMinorCounts

totalGametesNonMissingForTaxon

heterozygousCountForTaxon

totalNonMissingForTaxon

alleles

numberOfSites

numberOfTaxa

genotypeForAllSites

genotypeForSiteRange

siteStats

taxonStats

stream

stream

spliterator