Constant Field Values

Contents

• net.maizegenetics.*

net.maizegenetics.*

net.maizegenetics.analysis.association.AssociationConstants

Modifier and Type	Constant Field	Value
public static java.lang.String	STATS_HEADER_CHR	"Chr"
public static java.lang.String	STATS_HEADER_MARKER	"Marker"
public static java.lang.String	STATS_HEADER_POSITION	"Pos"
public static java.lang.String	STATS_HEADER_P_VALUE	"p"
public static java.lang.String	STATS_HEADER_TRAIT	"Trait"

net.maizegenetics.analysis.avro.AvroConstants

Modifier and Type	Constant Field	Value
public static int	GENOTYPE_BLOCK_SIZE	256
public static java.lang.String	POSITION_ALLELE_VALUE	"alleleValue"
public static java.lang.String	POSITION_CM	"cm"
public static java.lang.String	POSITION_IS_INDEL	"isIndel"
public static java.lang.String	POSITION_IS_NUCLEOTIDE	"isNucleotide"
public static java.lang.String	POSITION_MAF	"maf"
public static java.lang.String	POSITION_SITE_COVERAGE	"siteCoverage"
public static java.lang.String	POSITION_STRAND	"strand"

net.maizegenetics.analysis.data.FileLoadPlugin

Modifier and Type	Constant Field	Value
public static java.lang.String	FILE_EXT_FASTA	".fasta"
public static java.lang.String	FILE_EXT_HAPMAP	".hmp.txt"
public static java.lang.String	FILE_EXT_HAPMAP_GZ	".hmp.txt.gz"
public static java.lang.String	FILE_EXT_HAPMAP_GZ_LIX	".hmp.txt.gz.lix"
public static java.lang.String	FILE_EXT_HDF5	".h5"
public static java.lang.String	FILE_EXT_NEWICK	".nwk"
public static java.lang.String	FILE_EXT_PHYLIP	".phy"
public static java.lang.String	FILE_EXT_PLINK_MAP	".plk.map"
public static java.lang.String	FILE_EXT_PLINK_PED	".plk.ped"
public static java.lang.String	FILE_EXT_SERIAL_GZ	".serial.gz"
public static java.lang.String	FILE_EXT_TOPM	".topm"
public static java.lang.String	FILE_EXT_TOPM_BIN	".topm.bin"
public static java.lang.String	FILE_EXT_TOPM_H5	".topm.h5"
public static java.lang.String	FILE_EXT_TOPM_TEXT	".topm.txt"
public static java.lang.String	FILE_EXT_VCF	".vcf"

net.maizegenetics.analysis.filter.FilterTraitsDialog

Modifier and Type	Constant Field	Value
public static java.lang.String	CMD_CANCEL	"cancel"
public static java.lang.String	CMD_CHANGE_COV	"change2cov"
public static java.lang.String	CMD_CHANGE_DATA	"change2data"
public static java.lang.String	CMD_EXCLUDE	"exclude"
public static java.lang.String	CMD_EXCLUDE_ALL	"excludeall"
public static java.lang.String	CMD_INCLUDE	"include"
public static java.lang.String	CMD_INCLUDE_ALL	"includeall"
public static java.lang.String	CMD_OK	"ok"

net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin

Modifier and Type	Constant Field	Value
public static java.lang.String	rawSeqFileNameRegex	"(?i).*\\.fq$|.*\\.fq\\.gz$|.*\\.fastq$|.*_fastq\\.txt$|.*_fastq\\.gz$|.*_fastq\\.txt\\.gz$|.*_sequence\\.txt$|.*_sequence\\.txt\\.gz$|.*_qseq\\.txt$|.*_qseq\\.txt\\.gz$"

net.maizegenetics.analysis.gbs.TagMatchFinder

Modifier and Type	Constant Field	Value
public static int	maxDivergence	15
public static int	wordLength	16

net.maizegenetics.analysis.gbs.neobio.CharSequence

Modifier and Type	Constant Field	Value
public static char	COMMENT_CHAR	>

net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson

Modifier and Type	Constant Field	Value
public static byte	DIAGONAL_DIRECTION	2
public static byte	LEFT_DIRECTION	1
public static byte	STOP_DIRECTION	0
public static byte	TOP_DIRECTION	3

net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment

Modifier and Type	Constant Field	Value
public static byte	TYPE_CROSSING_PATH	0
public static byte	TYPE_C_PATH	2
public static byte	TYPE_E_PATH	3
public static byte	TYPE_S_PATH	1

net.maizegenetics.analysis.gbs.neobio.FactorSequence

Modifier and Type	Constant Field	Value
public static char	COMMENT_CHAR	>

net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm

Modifier and Type	Constant Field	Value
public static char	APPROXIMATE_MATCH_TAG	+
public static char	GAP_CHARACTER	-
public static char	GAP_TAG
public static char	MATCH_TAG	|
public static char	MISMATCH_TAG

net.maizegenetics.analysis.gbs.neobio.ScoringMatrix

Modifier and Type	Constant Field	Value
public static char	COMMENT_CHAR	#
public static char	INDEL_CHAR	*

net.maizegenetics.analysis.gbs.v2.GBSUtils

Modifier and Type	Constant Field	Value
public static java.lang.String	barcodeField	"Barcode"
public static java.lang.String	fileNameField	"FileName"
public static java.lang.String	flowcellField	"Flowcell"
public static java.lang.String	inputFileGlob	"glob:*{.fq,fq.gz,fastq,fastq.txt,fastq.gz,fastq.txt.gz,_sequence.txt,_sequence.txt.gz}"
public static java.lang.String	laneField	"Lane"
public static java.lang.String	sampleNameField	"FullSampleName"
public static java.lang.String	tissueNameField	"Tissue"

net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin

Modifier and Type	Constant Field	Value
public static java.lang.String	tab	"\t"

net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin

Modifier and Type	Constant Field	Value
public static java.lang.String	brkptComment1	"#Donor Haplotypes\n"
public static java.lang.String	brkptComment2	"#Taxa Breakpoints\n"
public static java.lang.String	brkptComment3	"#Block are defined chr:startPos:endPos:donor1:donor2 (-1 means no hypothesis)\n"

net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent

Modifier and Type	Constant Field	Value
public static int	DPRIME	1
public static int	P_VALUE	0
public static int	RSQUARE	2

net.maizegenetics.dna.BaseEncoder

Modifier and Type	Constant Field	Value
public static int	chunkSize	32
public static int	chunkSizeForInt	16

net.maizegenetics.dna.map.Position

Modifier and Type	Constant Field	Value
public static byte	STRAND_MINUS	0
public static java.lang.String	STRAND_MINUS_STR	"-"
public static byte	STRAND_PLUS	1
public static java.lang.String	STRAND_PLUS_STR	"+"
public static byte	STRAND_UNKNOWN	-128
public static java.lang.String	STRAND_UNKNOWN_STR	"N"

net.maizegenetics.dna.map.TOPMInterface

Modifier and Type	Constant Field	Value
public static byte	BYTE_MISSING	-128
public static int	INT_MISSING	-2147483648

net.maizegenetics.dna.snp.GenotypeTable

Modifier and Type	Constant Field	Value
public static java.lang.String	ANNOTATION_DATA_SET_DESCRIPTION	"dataSetDescription"
public static java.lang.String	ANNOTATION_DATA_SET_NAME	"dataSetName"

net.maizegenetics.dna.snp.HapMapHDF5Constants

Modifier and Type	Constant Field	Value
public static java.lang.String	ALLELES	"Alleles"
public static java.lang.String	ALLELE_CNT	"SiteDesc/AlleleCnt"
public static java.lang.String	ALLELE_FREQ_ORD	"SiteDesc/AlleleFreqOrder"
public static java.lang.String	ALLELE_STATES	"AlleleStates"
public static java.lang.String	BLOCK_SIZE	"blockSize"
public static java.lang.String	BPECAVGR2_DESC	"SiteDesc//ERROR/BPECR2"
public static java.lang.String	BPECERROR_DESC	"SiteDesc//ERROR/BPECERROR"
public static java.lang.String	BPLDMean34	"SiteDesc//LD/BPLDMean34R2"
public static java.lang.String	BPLDMeanMax	"SiteDesc//LD/BPLDMeanMaxR2"
public static java.lang.String	BPPopCnt	"SiteDesc//LD/BPPopCnt"
public static java.lang.String	BPmaxMaxLD	"SiteDesc//LD/BPmaxMaxLDR2"
public static java.lang.String	BPminMaxLD	"SiteDesc//LD/BPminMaxLDR2"
public static java.lang.String	DEFAULT_ATTRIBUTES_PATH	"/"
public static java.lang.String	DEPTH	"Depth"
public static java.lang.String	ERROR_DESC	"SiteDesc//ERROR"
public static java.lang.String	GENOMIC	"GenomeAnno"
public static java.lang.String	GENOTYPES	"Genotypes"
public static java.lang.String	GWAS	"GWAS"
public static java.lang.String	IBSERRORRATE_DESC	"SiteDesc//ERROR/IBSErrorRate"
public static java.lang.String	IBSERROR_DESC	"SiteDesc//ERROR/IBSError"
public static java.lang.String	IBSMAJORCORR_DESC	"SiteDesc//ERROR/IBSMajorCorrect"
public static java.lang.String	IBSMINORCORR_DESC	"SiteDesc//ERROR/IBSMinorCorrect"
public static java.lang.String	IBSMINORERRORRATE_DESC	"SiteDesc//ERROR/IBSMinorErrorRate"
public static java.lang.String	LDMinDist_DESC	"SiteDesc//LD/MinDist"
public static java.lang.String	LDP_DESC	"SiteDesc//LD/P"
public static java.lang.String	LDPropLD_DESC	"SiteDesc//LD/PropLD"
public static java.lang.String	LDR2_DESC	"SiteDesc//LD/R2"
public static java.lang.String	LD_BINS	"SiteDesc//LD/binsLD"
public static java.lang.String	LD_DESC	"SiteDesc//LD"
public static java.lang.String	LOCI	"SeqRegion"
public static java.lang.String	LOCUS_INDICES	"SeqRegionIndices"
public static java.lang.String	LOCUS_OFFSETS	"SeqRegionOffsets"
public static java.lang.String	MAF	"SiteDesc/MAF"
public static java.lang.String	MAJOR_ALLELE	"SiteDesc/MajorAllele"
public static java.lang.String	MAX_NUM_ALLELES	"maxNumAlleles"
public static java.lang.String	MINOR_ALLELE	"SiteDesc/MinorAllele"
public static java.lang.String	NUM_LD_BINS	"SiteDesc//LD/numLDBins"
public static java.lang.String	NUM_SBIT_WORDS	"numSBitWords"
public static java.lang.String	NUM_SITES	"numSites"
public static java.lang.String	NUM_TAXA	"numTaxa"
public static java.lang.String	NUM_TBIT_WORDS	"numTBitWords"
public static java.lang.String	POP_GEN	"PopGenAnno"
public static java.lang.String	POSITIONS	"Positions"
public static java.lang.String	REF_ALLELE	"SiteDesc/REFAllele"
public static java.lang.String	RETAIN_RARE_ALLELES	"retainRareAlleles"
public static java.lang.String	ROOT	"/"
public static java.lang.String	SBIT	"SBit"
public static java.lang.String	SITECOV	"SiteDesc/SiteCoverage"
public static java.lang.String	SITEHET	"SiteDesc/SiteHET"
public static java.lang.String	SITE_DESC	"SiteDesc/"
public static java.lang.String	SNP_IDS	"SnpIds"
public static java.lang.String	TAXA	"Taxa"
public static java.lang.String	TAXACOV	"TaxaDesc/TaxaCoverage"
public static java.lang.String	TAXAHET	"TaxaDesc/TaxaHet"
public static java.lang.String	TAXA_DESC	"TaxaDesc/"
public static java.lang.String	TBIT	"TBit"

net.maizegenetics.dna.snp.ImportUtils

Modifier and Type	Constant Field	Value
public static int	NUM_HAPMAP_NON_TAXA_HEADERS	11

net.maizegenetics.dna.snp.NucleotideAlignmentConstants

Modifier and Type	Constant Field	Value
public static byte	A_ALLELE	0
public static byte	A_DIPLOID_ALLELE	0
public static byte	C_ALLELE	1
public static byte	C_DIPLOID_ALLELE	17
public static byte	GAP_ALLELE	5
public static char	GAP_ALLELE_CHAR	-
public static java.lang.String	GAP_ALLELE_STR	"-"
public static byte	GAP_DIPLOID_ALLELE	85
public static byte	G_ALLELE	2
public static byte	G_DIPLOID_ALLELE	34
public static byte	INSERT_ALLELE	4
public static java.lang.String	INSERT_ALLELE_STR	"+"
public static byte	INSERT_DIPLOID_ALLELE	68
public static int	NUMBER_NUCLEOTIDE_ALLELES	6
public static byte	T_ALLELE	3
public static byte	T_DIPLOID_ALLELE	51
public static byte	UNDEFINED_ALLELE	6
public static java.lang.String	UNDEFINED_ALLELE_STR	"X"
public static byte	UNDEFINED_DIPLOID_ALLELE	102

net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache

Modifier and Type	Constant Field	Value
public static int	HETEROZYGOUS_COUNT	2
public static int	HOMOZYGOUS_COUNT	3
public static int	SITE_BLOCK_MASK	-256
public static int	UNKNOWN_COUNT	0
public static int	UNKNOWN_GAMETE_COUNT	1

net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable

Modifier and Type	Constant Field	Value
public static int	GENOTYPE_BLOCK_SIZE	256

net.maizegenetics.dna.snp.io.LineIndex

Modifier and Type	Constant Field	Value
public static int	NUM_LINES_PER_INTERVAL	10

net.maizegenetics.dna.snp.io.LineIndexBuilder

Modifier and Type	Constant Field	Value
public static java.lang.String	LINE_INDEX_FILE_EXTENSION	".lix"

net.maizegenetics.dna.snp.io.VCFUtil

Modifier and Type	Constant Field	Value
public static int	VCF_DEFAULT_MAX_NUM_ALLELES	3

net.maizegenetics.dna.snp.score.AlleleDepthUtil

Modifier and Type	Constant Field	Value
public static byte	DEPTH_BYTE_MISSING	-128
public static int	DEPTH_MISSING	-1

net.maizegenetics.dna.snp.score.SiteScoreUtil

Modifier and Type	Constant Field	Value
public static byte	BYTE_REPRESENTING_NAN	-1

net.maizegenetics.dna.tag.GBSHDF5Constants

Modifier and Type	Constant Field	Value
public static java.lang.String	BEST_CHR	"bestChr"
public static java.lang.String	BEST_DCOP	"bestDcoP"
public static java.lang.String	BEST_DIVERGENCE	"bestDivergence"
public static java.lang.String	BEST_ENDPOS	"bestEndPos"
public static java.lang.String	BEST_EVIDENCE	"bestEvidence"
public static java.lang.String	BEST_MAPINDEX	"bestMapIndex"
public static java.lang.String	BEST_MAPP	"bestMapP"
public static java.lang.String	BEST_STARTPOS	"bestStartPos"
public static java.lang.String	BEST_STRAND	"bestStrand"
public static java.lang.String	GENETICMAMMPING	"gm"
public static java.lang.String	GENETICMAMMPINGGW	"gmgw"
public static java.lang.String	MAPBASE	"map"
public static java.lang.String	MAXMAPPING	"maxMapping"
public static java.lang.String	MAXVARIANTS	"maxVariants"
public static java.lang.String	MULTIMAPS	"multimaps"
public static java.lang.String	ROOT	"/"
public static java.lang.String	TAGCOUNT	"tagCount"
public static java.lang.String	TAGLENGTH	"tagLength"
public static java.lang.String	TAGLENGTHINLONG	"tagLengthInLong"
public static java.lang.String	TAGS	"tags"
public static java.lang.String	VARIANTDEF	"variantDef"
public static java.lang.String	VARIANTPOSOFF	"variantPosOff"

net.maizegenetics.gui.PrintHeapAction

Modifier and Type	Constant Field	Value
public static java.lang.String	TEXT	"Show Memory"

net.maizegenetics.phenotype.CategoricalAttribute

Modifier and Type	Constant Field	Value
public static java.lang.String	missingValue	"?"

net.maizegenetics.phenotype.TaxaAttribute

Modifier and Type	Constant Field	Value
public static java.lang.String	DEFAULT_NAME	"Taxa"

net.maizegenetics.plugindef.AbstractPlugin

Modifier and Type	Constant Field	Value
public static java.lang.String	DEFAULT_CITATION	"Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635."
public static java.lang.String	POSITION_LIST_NONE	"None"
public static java.lang.String	TAXA_LIST_NONE	"None"

net.maizegenetics.prefs.TasselPrefs

Modifier and Type	Constant Field	Value
public static java.lang.String	ALIGNMENT_RETAIN_RARE_ALLELES	"retainRareAlleles"
public static boolean	ALIGNMENT_RETAIN_RARE_ALLELES_DEFAULT	false
public static java.lang.String	ALIGNMENT_TOP	"/tassel/alignment"
public static java.lang.String	BMS_DB	"bmsdb"
public static java.lang.String	BMS_DB_DEFAULT	""
public static java.lang.String	BMS_HOST	"bmshost"
public static java.lang.String	BMS_HOST_DEFAULT	"localhost"
public static java.lang.String	BMS_USER	"bmsuser"
public static java.lang.String	BMS_USER_DEFAULT	""
public static java.lang.String	EXPORT_PLUGIN_EXPORT_DIPLOIDS	"exportDiploids"
public static boolean	EXPORT_PLUGIN_EXPORT_DIPLOIDS_DEFAULT	false
public static java.lang.String	EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS	"includeTaxaAnnotations"
public static boolean	EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS_DEFAULT	true
public static java.lang.String	EXPORT_PLUGIN_TOP	"/tassel/plugins/export"
public static java.lang.String	FILTER_ALIGN_PLUGIN_MAX_FREQ	"maxFreq"
public static double	FILTER_ALIGN_PLUGIN_MAX_FREQ_DEFAULT	1.0
public static java.lang.String	FILTER_ALIGN_PLUGIN_MIN_COUNT	"minCount"
public static int	FILTER_ALIGN_PLUGIN_MIN_COUNT_DEFAULT	1
public static java.lang.String	FILTER_ALIGN_PLUGIN_MIN_FREQ	"minFreq"
public static double	FILTER_ALIGN_PLUGIN_MIN_FREQ_DEFAULT	0.0
public static java.lang.String	FILTER_ALIGN_PLUGIN_TOP	"/tassel/plugins/filterAlign"
public static java.lang.String	FILTER_TAXA_PROPS_PLUGIN_MAX_HET	"maxHetFreq"
public static double	FILTER_TAXA_PROPS_PLUGIN_MAX_HET_DEFAULT	1.0
public static java.lang.String	FILTER_TAXA_PROPS_PLUGIN_MIN_HET	"minHetFreq"
public static double	FILTER_TAXA_PROPS_PLUGIN_MIN_HET_DEFAULT	0.0
public static java.lang.String	FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING	"minNotMissingFreq"
public static double	FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING_DEFAULT	0.0
public static java.lang.String	FILTER_TAXA_PROPS_PLUGIN_TOP	"/tassel/plugins/filterTaxaAlign"
public static java.lang.String	GOBII_DB	"db"
public static java.lang.String	GOBII_DB_DEFAULT	""
public static java.lang.String	GOBII_TOP	"/tassel/gobii"
public static java.lang.String	GOBII_USER	"user"
public static java.lang.String	GOBII_USER_DEFAULT	""
public static java.lang.String	TASSEL_CONFIG_FILE	"configFile"
public static java.lang.String	TASSEL_CONFIG_FILE_DEFAULT	""
public static java.lang.String	TASSEL_LOCALE	"locale"
public static java.lang.String	TASSEL_LOG_DEBUG	"logDebug"
public static boolean	TASSEL_LOG_DEBUG_DEFAULT	false
public static java.lang.String	TASSEL_LOG_SEND_TO_CONSOLE	"logToConsole"
public static boolean	TASSEL_LOG_SEND_TO_CONSOLE_DEFAULT	false
public static java.lang.String	TASSEL_LOG_X_DIM	"logxDimension"
public static int	TASSEL_LOG_X_DIM_DEFAULT	-1
public static java.lang.String	TASSEL_LOG_Y_DIM	"logyDimension"
public static int	TASSEL_LOG_Y_DIM_DEFAULT	-1
public static java.lang.String	TASSEL_MAX_THREADS	"maxThreads"
public static java.lang.String	TASSEL_OPEN_DIR	"openDir"
public static java.lang.String	TASSEL_OPEN_DIR_DEFAULT	""
public static java.lang.String	TASSEL_SAVE_DIR	"saveDir"
public static java.lang.String	TASSEL_SAVE_DIR_DEFAULT	""
public static java.lang.String	TASSEL_TOP	"/tassel"
public static java.lang.String	TASSEL_X_DIM	"xDimension"
public static int	TASSEL_X_DIM_DEFAULT	-1
public static java.lang.String	TASSEL_Y_DIM	"yDimension"
public static int	TASSEL_Y_DIM_DEFAULT	-1

net.maizegenetics.stats.linearmodels.SweepFast

Modifier and Type	Constant Field	Value
public static double	TOL	1.0E-13

net.maizegenetics.tassel.DataTreePanel

Modifier and Type	Constant Field	Value
public static java.lang.String	NODE_TYPE_ASSOCIATIONS	"Association"
public static java.lang.String	NODE_TYPE_DATA	"Data"
public static java.lang.String	NODE_TYPE_DEFAULT	"Data"
public static java.lang.String	NODE_TYPE_DIVERSITY	"Diversity"
public static java.lang.String	NODE_TYPE_FILTERS	"Filters"
public static java.lang.String	NODE_TYPE_FUSIONS	"Fusions"
public static java.lang.String	NODE_TYPE_GENO_SUMMARY	"Genotype Summary"
public static java.lang.String	NODE_TYPE_HDF5_SCHEMA	"HDF5 Schema"
public static java.lang.String	NODE_TYPE_LD	"LD"
public static java.lang.String	NODE_TYPE_LISTS	"Lists"
public static java.lang.String	NODE_TYPE_MATRIX	"Matrix"
public static java.lang.String	NODE_TYPE_NUMERICAL	"Numerical"
public static java.lang.String	NODE_TYPE_POLYMORPHISMS	"Polymorphisms"
public static java.lang.String	NODE_TYPE_RESULT	"Result"
public static java.lang.String	NODE_TYPE_SEQUENCE	"Sequence"
public static java.lang.String	NODE_TYPE_SNP_ASSAYS	"SNP Assays"
public static java.lang.String	NODE_TYPE_STEPWISE	"Stepwise"
public static java.lang.String	NODE_TYPE_SYNONYMIZER	"Synonymizer"
public static java.lang.String	NODE_TYPE_SYNONYMS	"Synonyms"
public static java.lang.String	NODE_TYPE_TOPM	"TOPM"
public static java.lang.String	NODE_TYPE_TREE	"Tree"
public static java.lang.String	NODE_TYPE_VARIANCES	"Variances"

net.maizegenetics.tassel.TASSELMainFrame

Modifier and Type	Constant Field	Value
public static java.lang.String	version	"5.2.80"
public static java.lang.String	versionDate	"February 17, 2022"

net.maizegenetics.taxa.Taxon

Modifier and Type	Constant Field	Value
public static java.lang.String	AltitudeKey	"ALTITUDE"
public static java.lang.String	DELIMITER	":"
public static java.lang.String	FatherKey	"FATHER"
public static java.lang.String	GenusKey	"GENUS"
public static java.lang.String	InbreedFKey	"INBREEDF"
public static java.lang.String	LatitudeKey	"LATITUDE"
public static java.lang.String	LongitudeKey	"LONGITUDE"
public static java.lang.String	MotherKey	"MOTHER"
public static java.lang.String	PedigreeKey	"PEDIGREE"
public static java.lang.String	SexKey	"SEX"
public static java.lang.String	SpeciesKey	"SPECIES"
public static java.lang.String	SynonymKey	"SYNONYM"

net.maizegenetics.taxa.distance.DistanceMatrixBuilder

Modifier and Type	Constant Field	Value
public static java.lang.String	CENTERED_IBS_SUMPK	"Centered_IBS.SumPk"
public static java.lang.String	IBS_DISTANCE_MATRIX_AVE_TOTAL_SITES	"IBS_Distance_Matrix.AverageTotalSites"
public static java.lang.String	IBS_DISTANCE_MATRIX_NUM_ALLELES	"IBS_Distance_Matrix.NumAlleles"
public static java.lang.String	IBS_DISTANCE_MATRIX_TRUE_IBS	"IBS_Distance_Matrix.TrueIBS"
public static java.lang.String	IBS_DISTANCE_MATRIX_TYPE	"IBS_Distance_Matrix"
public static java.lang.String	MATRIX_ALGORITHM_VARIATION	"Matrix_Variation"
public static java.lang.String	MATRIX_TYPE	"Matrix_Type"

net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin

Modifier and Type	Constant Field	Value
public static java.lang.String	barcodeField	"Barcode"
public static java.lang.String	fileNameField	"FileName"
public static java.lang.String	flowcellField	"Flowcell"
public static java.lang.String	inputFileGlob	"glob:*{.fq,fq.gz,fastq,fastq.txt,fastq.gz,fastq.txt.gz,_sequence.txt,_sequence.txt.gz}"
public static java.lang.String	laneField	"Lane"
public static java.lang.String	sampleNameField	"FullSampleName"
public static java.lang.String	tissueNameField	"Tissue"

net.maizegenetics.util.ExceptionUtils

Modifier and Type	Constant Field	Value
public static int	DEFAULT_MAX_NUMBER_ENTRIES	50

net.maizegenetics.util.Tassel5HDF5Constants

Modifier and Type	Constant Field	Value
public static java.lang.String	ALLELE_CNT	"Genotypes/_Descriptors/AlleleCnt"
public static java.lang.String	ALLELE_FREQ_ORD	"Genotypes/_Descriptors/AlleleFreqOrder"
public static java.lang.String	ANC_ALLELES	"Positions/AncestralAlleles"
public static int	BLOCK_SIZE	65536
public static java.lang.String	CHROMOSOMES	"Positions/Chromosomes"
public static java.lang.String	CHROMOSOME_INDICES	"Positions/ChromosomeIndices"
public static java.lang.String	GENOTYPES_ALLELE_STATES	"Genotypes/AlleleStates"
public static java.lang.String	GENOTYPES_ATTRIBUTES_PATH	"Genotypes/"
public static java.lang.String	GENOTYPES_LOCKED	"locked"
public static java.lang.String	GENOTYPES_MAX_NUM_ALLELES	"maxNumAlleles"
public static java.lang.String	GENOTYPES_MODULE	"Genotypes"
public static java.lang.String	GENOTYPES_NUM_TAXA	"numTaxa"
public static java.lang.String	GENOTYPES_RETAIN_RARE_ALLELES	"retainRareAlleles"
public static java.lang.String	GENOTYPES_SCORE_TYPE	"scoreType"
public static java.lang.String	GENO_DESC	"Genotypes/_Descriptors/"
public static java.lang.String	MAF	"Genotypes/_Descriptors/MAF"
public static java.lang.String	POSITIONS	"Positions/Positions"
public static java.lang.String	POSITION_ATTRIBUTES_PATH	"Positions/"
public static java.lang.String	POSITION_GENOME_VERSION	"genomeVersion"
public static java.lang.String	POSITION_HAS_REFEFERENCE	"hasReferenceAlleles"
public static java.lang.String	POSITION_MODULE	"Positions"
public static java.lang.String	POSITION_NUM_SITES	"numSites"
public static java.lang.String	REF_ALLELES	"Positions/ReferenceAlleles"
public static java.lang.String	ROOT	"/"
public static java.lang.String	SITECOV	"Genotypes/_Descriptors/SiteCoverage"
public static java.lang.String	SNP_IDS	"Positions/SnpIds"
public static java.lang.String	TAGS	"Tags/Tags"
public static int	TAGS_BIN_NUM	64
public static java.lang.String	TAG_ATTRIBUTES_PATH	"Tags/"
public static java.lang.String	TAG_COUNT	"tagCount"
public static java.lang.String	TAG_DIST	"TagDist"
public static java.lang.String	TAG_DIST_OFFSETS	"TagTaxaDistOffset"
public static java.lang.String	TAG_LENGTHS	"TagLength"
public static java.lang.String	TAG_LENGTH_LONG	"tagLengthLong"
public static java.lang.String	TAG_LOCKED	"locked"
public static java.lang.String	TAG_MODULE	"Tags"
public static java.lang.String	TAG_SEQ	"TagSeq"
public static java.lang.String	TAXACOV	"Genotypes/_Descriptors/TaxaCoverage"
public static java.lang.String	TAXAHET	"Genotypes/_Descriptors/TaxaHet"
public static java.lang.String	TAXA_ATTRIBUTES_PATH	"Taxa/"
public static java.lang.String	TAXA_LOCKED	"locked"
public static java.lang.String	TAXA_MODULE	"Taxa"
public static java.lang.String	TAXA_NUM_TAXA	"numTaxa"
public static java.lang.String	TAXA_ORDER	"Taxa/TaxaOrder"