HapMapHDF5Constants (net.maizegenetics:tassel 5.2.49 API)

java.lang.Object
- net.maizegenetics.dna.snp.HapMapHDF5Constants

Deprecated.
```
@Deprecated
public final class HapMapHDF5Constants
extends Object
```
Definition of fields and directories of the GenotypeTable in a HDF5 file format.

Author:

Terry Casstevens

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`ALLELE_CNT` Deprecated.
`static String`	`ALLELE_FREQ_ORD` Deprecated.
`static String`	`ALLELE_STATES` Deprecated.
`static String`	`ALLELES` Deprecated.
`static String`	`BLOCK_SIZE` Deprecated.
`static String`	`BPECAVGR2_DESC` Deprecated.
`static String`	`BPECERROR_DESC` Deprecated.
`static String`	`BPLDMean34` Deprecated.
`static String`	`BPLDMeanMax` Deprecated.
`static String`	`BPmaxMaxLD` Deprecated.
`static String`	`BPminMaxLD` Deprecated.
`static String`	`BPPopCnt` Deprecated.
`static String`	`DEFAULT_ATTRIBUTES_PATH` Deprecated.
`static String`	`DEPTH` Deprecated.
`static String`	`ERROR_DESC` Deprecated.
`static ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures`	`floatDeflation` Deprecated.
`static ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures`	`genDeflation` Deprecated.
`static String`	`GENOMIC` Deprecated.
`static String`	`GENOTYPES` Deprecated.
`static String`	`GWAS` Deprecated.
`static String`	`IBSERROR_DESC` Deprecated.
`static String`	`IBSERRORRATE_DESC` Deprecated.
`static String`	`IBSMAJORCORR_DESC` Deprecated.
`static String`	`IBSMINORCORR_DESC` Deprecated.
`static String`	`IBSMINORERRORRATE_DESC` Deprecated.
`static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures`	`intDeflation` Deprecated.
`static String`	`LD_BINS` Deprecated.
`static String`	`LD_DESC` Deprecated.
`static String`	`LDMinDist_DESC` Deprecated.
`static String`	`LDP_DESC` Deprecated.
`static String`	`LDPropLD_DESC` Deprecated.
`static String`	`LDR2_DESC` Deprecated.
`static String`	`LOCI` Deprecated.
`static String`	`LOCUS_INDICES` Deprecated.
`static String`	`LOCUS_OFFSETS` Deprecated.
`static String`	`MAF` Deprecated.
`static String`	`MAJOR_ALLELE` Deprecated.
`static String`	`MAX_NUM_ALLELES` Deprecated.
`static String`	`MINOR_ALLELE` Deprecated.
`static String`	`NUM_LD_BINS` Deprecated.
`static String`	`NUM_SBIT_WORDS` Deprecated.
`static String`	`NUM_SITES` Deprecated.
`static String`	`NUM_TAXA` Deprecated.
`static String`	`NUM_TBIT_WORDS` Deprecated.
`static String`	`POP_GEN` Deprecated.
`static String`	`POSITIONS` Deprecated.
`static String`	`REF_ALLELE` Deprecated.
`static String`	`RETAIN_RARE_ALLELES` Deprecated.
`static String`	`ROOT` Deprecated.
`static String`	`SBIT` Deprecated.
`static String`	`SITE_DESC` Deprecated.
`static String`	`SITECOV` Deprecated.
`static String`	`SITEHET` Deprecated.
`static String`	`SNP_IDS` Deprecated.
`static String`	`TAXA` Deprecated.
`static String`	`TAXA_DESC` Deprecated.
`static String`	`TAXACOV` Deprecated.
`static String`	`TAXAHET` Deprecated.
`static String`	`TBIT` Deprecated.

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

- Field Detail
  - ROOT
```
public static final String ROOT
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - TAXA
```
public static final String TAXA
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ALLELE_STATES
```
public static final String ALLELE_STATES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - POSITIONS
```
public static final String POSITIONS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ALLELES
```
public static final String ALLELES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - TBIT
```
public static final String TBIT
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SBIT
```
public static final String SBIT
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - DEPTH
```
public static final String DEPTH
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - GENOTYPES
```
public static final String GENOTYPES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LOCI
```
public static final String LOCI
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LOCUS_OFFSETS
```
public static final String LOCUS_OFFSETS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LOCUS_INDICES
```
public static final String LOCUS_INDICES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SNP_IDS
```
public static final String SNP_IDS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SITE_DESC
```
public static final String SITE_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ALLELE_CNT
```
public static final String ALLELE_CNT
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - MAF
```
public static final String MAF
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SITECOV
```
public static final String SITECOV
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - SITEHET
```
public static final String SITEHET
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - MAJOR_ALLELE
```
public static final String MAJOR_ALLELE
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - MINOR_ALLELE
```
public static final String MINOR_ALLELE
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ALLELE_FREQ_ORD
```
public static final String ALLELE_FREQ_ORD
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - REF_ALLELE
```
public static final String REF_ALLELE
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - TAXA_DESC
```
public static final String TAXA_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - TAXACOV
```
public static final String TAXACOV
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - TAXAHET
```
public static final String TAXAHET
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LD_DESC
```
public static final String LD_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LDR2_DESC
```
public static final String LDR2_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LDP_DESC
```
public static final String LDP_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LDPropLD_DESC
```
public static final String LDPropLD_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LDMinDist_DESC
```
public static final String LDMinDist_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BPLDMean34
```
public static final String BPLDMean34
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BPLDMeanMax
```
public static final String BPLDMeanMax
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BPmaxMaxLD
```
public static final String BPmaxMaxLD
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BPminMaxLD
```
public static final String BPminMaxLD
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BPPopCnt
```
public static final String BPPopCnt
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - ERROR_DESC
```
public static final String ERROR_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BPECERROR_DESC
```
public static final String BPECERROR_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BPECAVGR2_DESC
```
public static final String BPECAVGR2_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - IBSERRORRATE_DESC
```
public static final String IBSERRORRATE_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - IBSMINORERRORRATE_DESC
```
public static final String IBSMINORERRORRATE_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - IBSERROR_DESC
```
public static final String IBSERROR_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - IBSMINORCORR_DESC
```
public static final String IBSMINORCORR_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - IBSMAJORCORR_DESC
```
public static final String IBSMAJORCORR_DESC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_ATTRIBUTES_PATH
```
public static final String DEFAULT_ATTRIBUTES_PATH
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NUM_SBIT_WORDS
```
public static final String NUM_SBIT_WORDS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NUM_TBIT_WORDS
```
public static final String NUM_TBIT_WORDS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NUM_TAXA
```
public static final String NUM_TAXA
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NUM_SITES
```
public static final String NUM_SITES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - BLOCK_SIZE
```
public static final String BLOCK_SIZE
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - MAX_NUM_ALLELES
```
public static final String MAX_NUM_ALLELES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - RETAIN_RARE_ALLELES
```
public static final String RETAIN_RARE_ALLELES
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - NUM_LD_BINS
```
public static final String NUM_LD_BINS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - LD_BINS
```
public static final String LD_BINS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - intDeflation
```
public static final ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures intDeflation
```
    Deprecated.
  - genDeflation
```
public static final ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures genDeflation
```
    Deprecated.
  - floatDeflation
```
public static final ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures floatDeflation
```
    Deprecated.
  - GWAS
```
public static final String GWAS
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - GENOMIC
```
public static final String GENOMIC
```
    Deprecated.
    
    See Also:
    
    Constant Field Values
  - POP_GEN
```
public static final String POP_GEN
```
    Deprecated.
    
    See Also:
    
    Constant Field Values

Class HapMapHDF5Constants

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ROOT

TAXA

ALLELE_STATES

POSITIONS

ALLELES

TBIT

SBIT

DEPTH

GENOTYPES

LOCI

LOCUS_OFFSETS

LOCUS_INDICES

SNP_IDS

SITE_DESC

ALLELE_CNT

MAF

SITECOV

SITEHET

MAJOR_ALLELE

MINOR_ALLELE

ALLELE_FREQ_ORD

REF_ALLELE

TAXA_DESC

TAXACOV

TAXAHET

LD_DESC

LDR2_DESC

LDP_DESC

LDPropLD_DESC

LDMinDist_DESC

BPLDMean34

BPLDMeanMax

BPmaxMaxLD

BPminMaxLD

BPPopCnt

ERROR_DESC

BPECERROR_DESC

BPECAVGR2_DESC

IBSERRORRATE_DESC

IBSMINORERRORRATE_DESC

IBSERROR_DESC

IBSMINORCORR_DESC

IBSMAJORCORR_DESC

DEFAULT_ATTRIBUTES_PATH

NUM_SBIT_WORDS

NUM_TBIT_WORDS

NUM_TAXA

NUM_SITES

BLOCK_SIZE

MAX_NUM_ALLELES

RETAIN_RARE_ALLELES

NUM_LD_BINS

LD_BINS

intDeflation

genDeflation

floatDeflation

GWAS

GENOMIC

POP_GEN