Uses of Class
net.maizegenetics.util.Tuple

Packages that use Tuple

Package	Description
net.maizegenetics.analysis.gbs.repgen
net.maizegenetics.analysis.phg
net.maizegenetics.analysis.rna
net.maizegenetics.dna.map	Supports genetic and physical map representations of genomes including their annotation.
net.maizegenetics.dna.snp	Data structures for holding SNP and indel variation across taxa (samples) and genomic positions.
net.maizegenetics.dna.snp.genotypecall	Genotype calls for all the taxa and genomic positions scored.
net.maizegenetics.dna.snp.io	Support for reading and writing GenotypeTables to various file formats.
net.maizegenetics.dna.tag	Data structures for holding tags (contiguous DNA).
net.maizegenetics.util	Provide basic utilities classes and methods used the entire code base.

Uses of Tuple in net.maizegenetics.analysis.gbs.repgen

Methods in net.maizegenetics.analysis.gbs.repgen that return types with arguments of type Tuple

Modifier and Type	Method and Description
static Map<Tag,Tuple<Integer,String>>	RepGenLoadSeqToDBPlugin.calculateTagAveQS(RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap tagCntQSMap, int qualityScoreBase)

Uses of Tuple in net.maizegenetics.analysis.phg

Methods in net.maizegenetics.analysis.phg that return Tuple

Modifier and Type	Method and Description
static Tuple<List<String>,BlockingQueue<Future<ParseGVCF.ProcessLines>>>	ParseGVCF.parse(String filename)
static Tuple<List<String>,Stream<ParseGVCF.GVCFLine>>	ParseGVCF.stream(String filename) The returns a list of the GVCF header lines and a stream of the processed data lines.

Uses of Tuple in net.maizegenetics.analysis.rna

Methods in net.maizegenetics.analysis.rna that return Tuple

Modifier and Type	Method and Description
static Tuple<Integer,Integer>	FindMatchByWordHash.calcIdentity(String querySeq, String refSeq)

Uses of Tuple in net.maizegenetics.dna.map

Methods in net.maizegenetics.dna.map that return Tuple

Modifier and Type	Method and Description
Tuple<PositionList,int[]>	PositionListBuilder.buildWithSiteRedirect()

Methods in net.maizegenetics.dna.map that return types with arguments of type Tuple

Modifier and Type	Method and Description
Map<Long,Tuple<Chromosome,Integer>>	GenomeSequence.fullRefCoordinateToChromCoordinate(ArrayList<Long> coordinates) Takes a list of coordinates from the full genome sequence and for each returns the corresponding chromosome and a coordinate relative to the start of that chromosome.

Uses of Tuple in net.maizegenetics.dna.snp

Methods in net.maizegenetics.dna.snp that return Tuple

Modifier and Type	Method and Description
static Tuple<GenotypeTable,double[]>	FilterGenotypeTable.getInstanceTaxaOrderedByGeneticDistance(GenotypeTable genotypes, int taxon)

Uses of Tuple in net.maizegenetics.dna.snp.genotypecall

Methods in net.maizegenetics.dna.snp.genotypecall that return Tuple

Modifier and Type	Method and Description
static Tuple<GenotypeCallTable,Translate>	GenotypeCallTableBuilder.getFilteredInstance(GenotypeCallTable genotype, Translate translate)

Uses of Tuple in net.maizegenetics.dna.snp.io

Methods in net.maizegenetics.dna.snp.io that return Tuple

Modifier and Type	Method and Description
static Tuple<LineIndex,String[]>	LineIndexBuilder.readIndex(String idxFilename)
static Tuple<int[],String[]>	VCFUtil.resolveSortedAndKnownVariantsExport(int[] sortedAllelesInput, String[] knownVariantsInput)

Uses of Tuple in net.maizegenetics.dna.tag

Methods in net.maizegenetics.dna.tag that return types with arguments of type Tuple

Modifier and Type	Method and Description
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	RepGenData.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition) Map of positions and with associated map of Tags and their taxa distribution and their alignment direction.
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	RepGenSQLite.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition)
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	TagData.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition) Map of positions and with associated map of Tags and their taxa distribution and their alignment direction.
Map<Position,Map<Tag,Tuple<Boolean,TaxaDistribution>>>	TagDataSQLite.getCutPositionTagTaxaMap(Chromosome chromosome, int firstPosition, int lastPosition)
com.google.common.collect.ListMultimap<String,Tuple<Integer,Float>>	RepGenData.getSNPPositionQS(com.google.common.collect.HashMultimap<String,Integer> myMap) For a given map of chromosome/posiiton, Returns a map of chromsome (string) and Tuple (position,qualityScore)
com.google.common.collect.ListMultimap<String,Tuple<Integer,Float>>	RepGenSQLite.getSNPPositionQS(com.google.common.collect.HashMultimap<String,Integer> myMap)
com.google.common.collect.ListMultimap<String,Tuple<Integer,Float>>	TagData.getSNPPositionQS(com.google.common.collect.HashMultimap<String,Integer> myMap) For a given map of chromosome/posiiton, Returns a map of chromsome (string) and Tuple (position,qualityScore)
com.google.common.collect.ListMultimap<String,Tuple<Integer,Float>>	TagDataSQLite.getSNPPositionQS(com.google.common.collect.HashMultimap<String,Integer> myMap)

Method parameters in net.maizegenetics.dna.tag with type arguments of type Tuple

Modifier and Type	Method and Description
void	RepGenDataWriter.putAllelePairs(com.google.common.collect.Multimap<Tag,Tuple<Tag,Integer>> tagTagAlignMap) Adds entries to the allelepair table
void	RepGenSQLite.putAllelePairs(com.google.common.collect.Multimap<Tag,Tuple<Tag,Integer>> tagTagAlignMap)
boolean	RepGenDataWriter.putAllTag(Set<Tag> tags, Map<Tag,Tuple<Integer,String>> tagInstanceAverageQS) Add a tag to list of known tags
boolean	RepGenSQLite.putAllTag(Set<Tag> tags, Map<Tag,Tuple<Integer,String>> tagInstanceAverageQS)

Uses of Tuple in net.maizegenetics.util

Methods in net.maizegenetics.util that return Tuple

Modifier and Type	Method and Description
static <T> Tuple<ArrayList<Tuple<T,T>>,ArrayList<Byte>>	GraphUtils.dfsLabeledEdges(Graph<T> G, T source) Produces edges in a depth-first search starting at source and labeled -1,0,1 for forward, reverse, and nontree (direction type).

Methods in net.maizegenetics.util that return types with arguments of type Tuple

Modifier and Type	Method and Description
static <T> Tuple<ArrayList<Tuple<T,T>>,ArrayList<Byte>>	GraphUtils.dfsLabeledEdges(Graph<T> G, T source) Produces edges in a depth-first search starting at source and labeled -1,0,1 for forward, reverse, and nontree (direction type).

Methods in net.maizegenetics.util with parameters of type Tuple

Modifier and Type	Method and Description
int	Tuple.compareTo(Tuple<X,Y> o) Using this method (i.e.

Constructor parameters in net.maizegenetics.util with type arguments of type Tuple

Constructor and Description
DirectedGraph(HashSet<T> nodes, com.google.common.collect.ImmutableSetMultimap<T,T> adj, com.google.common.collect.ImmutableSetMultimap<T,T> pred, HashMap<Tuple<T,T>,Double> wts)
UndirectedGraph(HashSet<T> nodes, com.google.common.collect.ImmutableSetMultimap<T,T> adj, HashMap<Tuple<T,T>,Double> wts) Constructs an undirected graph