A B C D E F G H I J K L M N O P Q R S T U V W X Z

N

NEBParser - class util.bio.digest.NEBParser.

Parses a New England Biolabs restriction enzyme file into an array of Enzymes.

NEBParser() - Constructor for class util.bio.digest.NEBParser

NO_OPTIONS - Static variable in class com.amazon.thirdparty.Base64

No options specified.

NewAntibody - class bioroot.antibody.NewAntibody.

NewAntibody() - Constructor for class bioroot.antibody.NewAntibody

NewOligo - class bioroot.oligo.NewOligo.

NewOligo() - Constructor for class bioroot.oligo.NewOligo

NewPlasmid - class bioroot.plasmid.NewPlasmid.

NewPlasmid() - Constructor for class bioroot.plasmid.NewPlasmid

NewStrain - class bioroot.strain.NewStrain.

NewStrain() - Constructor for class bioroot.strain.NewStrain

NucleicAcid - class util.bio.calc.NucleicAcid.

Nucleic Acid parameter calculator and converter static methods.

NucleicAcid() - Constructor for class util.bio.calc.NucleicAcid

Num - class util.gen.Num.

Math and statistical static methods.

Num() - Constructor for class util.gen.Num

name - Variable in class com.amazon.s3.Bucket

The name of the bucket.

name - Variable in class com.amazon.s3.ListBucketResponse

The name of the bucket being listed.

nameParser - Static variable in class util.bio.seq.IndexedSequence

nearestNeighborOligoTm(String, double, double) - Static method in class util.bio.calc.NucleicAcid

Calculates nearest neighbor tm given a DNA oligonucleotide.

newUseDilutionIndex(AntibodyBean, DBUtil, HashMap) - Static method in class bioroot.antibody.AntibodyBase

Scans a hashmap for a newUseDilution selection, returns the index number

nextMarker - Variable in class com.amazon.s3.ListBucketResponse

Indicates what to use as a marker for subsequent list requests in the event that the results are truncated.

nonAmbiguousLetters - Static variable in class util.gen.Passwords

normalizeCelFiles() - Method in class trans.main.T2

normalizeQuantileArrayScores(Quantile[][]) - Static method in class trans.cel.QuantileNormalization

Takes arrays of Quantile, and averages the values for a given array index.

nullArrays() - Method in class util.gen.LinearRegression

Nulls the x and y arrays.

nullIndexedSequences() - Method in class util.bio.seq.FetchIndexedSequence

Good to call after each call to fetchSequences() unless you'll be fetching more from the same chromosome.

nullIntensityArrays() - Method in class trans.qc.CelFileStats

Nulls the virtualCel and collapsed intensities array.

numberBases(BindingRegion[]) - Static method in class trans.anno.IntersectRegions

numberBases(BindingRegion[]) - Static method in class util.bio.parsers.FetchGenomicSequences

numberBinHitsToLeftAndIncludingValue(double) - Method in class util.gen.Histogram

Returns number of bin hits in the bins to the right of the value's bin including the numMoreThanMax.

numberBinHitsToRightAndIncludingValue(double) - Method in class util.gen.Histogram

Returns number of bin hits in the bins to the right of the value's bin including the numMoreThanMax.

numberBinHitsToRightOfValue(double) - Method in class util.gen.Histogram

Returns number of bin hits in the bins to the right of the value's bin including the numMoreThanMax.

numberFilesExist(File, String) - Static method in class util.gen.IO

Returns the number of files that end with the given extension.

numberFilesExist(File[]) - Static method in class util.gen.IO

Returns the number of files that exist in the array.

numberLetters - Static variable in class util.gen.Passwords

numberOfIntervalsToMake() - Method in class trans.main.T2

Returns the number of intervals that remain to be made.

numberReplicasToMake() - Method in class trans.main.T2

numberUniqueValues(int[], int, int) - Static method in class trans.tpmap.WindowMaker

Given a sorted set of values, a start and stop index (inclusive) returns the number of unique values.