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

I

IO - class util.gen.IO.

Static methods for Input Output related tasks.

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

IPPort - Static variable in class bioroot.Util

IPPort - Static variable in class util.gen.SQL

CHANGEME IP and Port

IdNameMatch - class bioroot.IdNameMatch.

IdNameMatch(int, String) - Constructor for class bioroot.IdNameMatch

IndexFastas - class util.bio.seq.IndexFastas.

IndexFastas(String[]) - Constructor for class util.bio.seq.IndexFastas

IndexRegions - class util.bio.seq.IndexRegions.

IndexRegions() - Constructor for class util.bio.seq.IndexRegions

IndexedSequence - class util.bio.seq.IndexedSequence.

IndexedSequence(File) - Constructor for class util.bio.seq.IndexedSequence

InefficientPseudoMedian - class trans.misc.InefficientPseudoMedian.

InefficientPseudoMedian() - Constructor for class trans.misc.InefficientPseudoMedian

IntensityFeature - class trans.tpmap.IntensityFeature.

Minimal info about a feature for combining multiple chips together.

IntensityFeature(MapFeature, float) - Constructor for class trans.tpmap.IntensityFeature

IntensityPrinter - class trans.main.IntensityPrinter.

Prints out processed '.celp' files as '.sgr' files for import into Affy's IGB.

IntensityPrinter(String[]) - Constructor for class trans.main.IntensityPrinter

IntersectBindingPeaks - class trans.anno.IntersectBindingPeaks.

Performs an intersection analysis on two peak pick files (chr peakPosition score).

IntersectBindingPeaks(String[]) - Constructor for class trans.anno.IntersectBindingPeaks

IntersectKeyWithRegions - class trans.anno.IntersectKeyWithRegions.

Takes a key from a spike in experiment and sorted lists of regions to calculate TPR, FPR, and FDR for every threshold

IntersectKeyWithRegions(String[]) - Constructor for class trans.anno.IntersectKeyWithRegions

IntersectLists - class util.apps.IntersectLists.

Compares two lists of words for intersection.

IntersectLists() - Constructor for class util.apps.IntersectLists

IntersectRegions - class trans.anno.IntersectRegions.

Performs an intersection analysis on binding region files (chr start stop (optional fraction gc)).

IntersectRegions(String[]) - Constructor for class trans.anno.IntersectRegions

Interval - class trans.main.Interval.

Container for holding information about a potential enriched region: windows, oligos, sub windows, binding peaks....

Interval(Window, int) - Constructor for class trans.main.Interval

IntervalComparator - class trans.main.IntervalComparator.

Class to help sort an array of Interval[] by chromosome, start position, length shortest first.

IntervalComparator() - Constructor for class trans.main.IntervalComparator

IntervalDrawFrame - class trans.graphics.IntervalDrawFrame.

Frame for IntervalPlotter.

IntervalDrawFrame() - Constructor for class trans.graphics.IntervalDrawFrame

IntervalDrawFrame(Interval, int, TextFrame, boolean) - Constructor for class trans.graphics.IntervalDrawFrame

IntervalDrawPanel - class trans.graphics.IntervalDrawPanel.

Panel with the meat for IntervalPlotter

IntervalDrawPanel(Interval, int, TextFrame, boolean) - Constructor for class trans.graphics.IntervalDrawPanel

IntervalFilter - class trans.main.IntervalFilter.

Sorts an Interval[] into two groups, those that pass or fail a variety of filters.

IntervalFilter(String[]) - Constructor for class trans.main.IntervalFilter

IntervalGFFPrinter - class trans.main.IntervalGFFPrinter.

Prints intervals as a GFF3 File.

IntervalGFFPrinter(String[]) - Constructor for class trans.main.IntervalGFFPrinter

IntervalGraphPrinter - class trans.main.IntervalGraphPrinter.

Prints an array of Interval as an '.sgr' file for import into IGB.

IntervalGraphPrinter(String[]) - Constructor for class trans.main.IntervalGraphPrinter

IntervalMaker - class trans.main.IntervalMaker.

Collapses an array of Window into and array of Interval based on scores.

IntervalMaker(String[]) - Constructor for class trans.main.IntervalMaker

IntervalMaker(File, Window[], double[], int, int, int, int) - Constructor for class trans.main.IntervalMaker

IntervalPlotter - class trans.graphics.IntervalPlotter.

Application to draw graphical representations of loaded Intervals.

IntervalPlotter(String[]) - Constructor for class trans.graphics.IntervalPlotter

IntervalReportPrinter - class trans.main.IntervalReportPrinter.

Prints all things contained within an interval to a spreadsheet or a report card.

IntervalReportPrinter(String[]) - Constructor for class trans.main.IntervalReportPrinter

id - Variable in class com.amazon.s3.Owner

identifyOutliers(float[][], int[][], float, boolean) - Static method in class util.gen.Num

Loads a zeroed matrix with values that are > or < threshold based on boolean.

igb.util - package igb.util

Utilities for converting TiMAT results into Affymetrix IGB visualizations.

importScores(Window[], File) - Method in class trans.main.ScanChip

Reads in a file of scores from a qvalue output file Also writes and zips an .sgr file for the qValues.

importScores(Window[], File) - Method in class trans.main.ScanChromosomes

Reads in a file of scores from a qvalue output file Also makes gr files for the qValues.

inRegion(Sgr, Positive[]) - Static method in class trans.roc.ParseBarsForParticularRegions

Checks to see if an sgr object is in one of the positives, if not returns -1, otherwise returns index number.

inRegion(Sgr, Positive[]) - Static method in class trans.roc.ParseSgrsForParticularRegions

Checks to see if an sgr object is in one of the positives, if not returns -1, otherwise returns index number.

incNumFiles(int) - Method in class selex.SelexParams

incNumSeqReads(int) - Method in class selex.SelexParams

incNumSubs(int, int, int) - Method in class selex.SelexParams

incrementNegatives() - Method in class trans.roc.Bin

incrementNumBadSeqReads() - Method in class selex.SelexParams

incrementNumNoInsertSeqReads() - Method in class selex.SelexParams

incrementNumShortInsertSeqReads() - Method in class selex.SelexParams

incrementPositives() - Method in class trans.roc.Bin

index() - Method in class util.bio.seq.IndexFastas

initializeTrackLabels() - Method in class gata.geneGlyphs.Annotation

instantiateStatFlags() - Method in class trans.qc.CelFileQualityControl

Makes the Stat Flags, add new stats here.

intArrayToString(int[], String) - Static method in class util.gen.Misc

Returns a String separated by separator for each int[i].

intArrayToString(int[], String) - Static method in class util.gen.Num

Converts an array of int to a String seperated by the delimiter.

integerArrayListToIntArray(ArrayList) - Static method in class util.gen.Misc

Converts an ArrayList of Integer to int[].

intensity - Variable in class trans.tpmap.IntensityFeature

interpolate(int, double) - Method in class util.gen.CubicSpline

Returns a cubic-spline interpolated value y for the point between point (n, y[n]) and (n+1, y[n+1), with t ranging from 0 for (n, y[n]) to 1 for (n+1, y[n+1]).

interpolateX(double, double, double, double, double) - Static method in class util.gen.LinearRegression

Return approximated X value, good for a single interpolation, multiple calls are inefficient!

interpolateY(double, double, double, double, double) - Static method in class util.gen.LinearRegression

Return approximated Y value, good for a single interpolation, multiple calls are inefficient!

interrogate() - Method in class util.apps.Flash

intersect(Interval) - Method in class trans.anno.Region

intersect(TPMapLine) - Method in class trans.anno.Region

intersect(Window, int, double) - Method in class trans.anno.Region

Returns true only if region contains or is contained or is covered by >= fractionAcceptibleCoverage by a window.

intersect() - Method in class trans.graphics.RankedSetAnalysis

intersectBindingRegions() - Method in class trans.anno.IntersectRegions

intersectRandomBindingRegions(BindingRegion[], BindingRegion[]) - Method in class trans.anno.IntersectRegions

Assumes the same chromosome

intersectRandomRegions() - Method in class trans.anno.IntersectRegions

Increments the hitsPerTrial int[].

intersectRegions() - Method in class trans.graphics.RankedSetAnalysis

Loads regions with references to intersection partners.

intersectReturnBP(BindingRegion) - Method in class trans.anno.BindingRegion

Returns -1 for no overlap or the # bases of intersection.

intersectReturnGap(BindingRegion) - Method in class trans.anno.BindingRegion

Returns -1 if on diff chromosomes, 0 if they overlap, or the # of bases between the two.

intersects(BindingRegion) - Method in class trans.anno.BindingRegion

intersects(RocWindow) - Method in class trans.roc.RocWindow

intersectsKey(Region) - Method in class trans.anno.IntersectKeyWithRegions

Returns 1 if bpInt <= maxGap and the particular key hasn't been hit, 0 not in key, -1 hits a key that has already been counted.

invertArray(float[]) - Static method in class util.gen.Num

Inverts the float[].

invertScores(Window[]) - Static method in class trans.main.IntervalMaker

Multiplies all of the Window[] scores by -1

isAntibodyNameUnique(DBUtil) - Method in class bioroot.antibody.AntibodyBean

checks to see if antibody name is unique within labgroup, assumes a connection has been made

isArchived() - Method in class bioroot.LabGroup

isBestWindowScored() - Method in class trans.main.Interval

isBlasted() - Method in class bioroot.plasmid.PlasmidBean

isBroken() - Method in class util.apps.HouseBean

isCompVisible() - Method in class gata.aligner.AlignParams

isCompVisible() - Method in class gata.aligner.Alignment

isComplete() - Method in class bioroot.CellTypeBean

isComplete() - Method in class bioroot.GeneBean

isComplete() - Method in class bioroot.MarkerBean

isComplete() - Method in class bioroot.OrganismBean

isComplete() - Method in class bioroot.ReagentBean

isComplete() - Method in class bioroot.UserRegistrationBean

isComplete() - Method in class bioroot.oligo.OligoUploadBean

isComplete() - Method in class bioroot.plasmid.PlasmidUploadBean

isComplete() - Method in class bioroot.strain.StrainUploadBean

isConnected() - Method in class util.amazon.S3Manager

isConnectionClosed() - Method in class bioroot.DBUtil

checks if the connection is open

isDNAVis() - Method in class gata.main.GATAParams

isEXTRACT() - Method in class gata.aligner.AlignParams

isEmpty(String) - Static method in class gata.main.GATAUtil

Method to check if a string is null or empty after trimming

isEmpty(String) - Static method in class util.gen.Misc

Method to check if a string is null or empty after trimming.

isEndSet() - Method in class util.bio.parsers.gff.Gff3Feature

isExistingMember() - Method in class bioroot.UserRegistrationBean

isFastaFound() - Method in class util.bio.parsers.MultiFastaParser

isGenericFeaturesFound() - Method in class util.bio.parsers.gff.DmelRel4Extractor

isGenericFeaturesFound() - Method in class util.bio.parsers.gff.GadFlyGffExtractor

isGenericLabelsVis() - Method in class gata.main.GATAParams

isGffCompPresent() - Method in class gata.main.GATAParams

isGffGood() - Method in class util.bio.parsers.gff.GffFeature

isGffRefPresent() - Method in class gata.main.GATAParams

isGuest() - Method in class bioroot.UserBean

isGuestOrFriend() - Method in class bioroot.UserBean

isInPeak() - Method in class trans.main.Oligo

isLabelsVis() - Method in class gata.main.GATAParams

isLoginNameUnique() - Method in class bioroot.UserRegistrationBean

checks to see if login name is unique, assumes a connection has been made

isMakeChallenge() - Method in class bioroot.LoginBean

isMakeReducedWindows() - Method in class trans.main.T2Parameter

isMedianScaleUsingControlSeqs() - Method in class trans.main.T2Parameter

isNameChanged() - Method in class bioroot.antibody.AntibodyBean

isNameUnique(String, String) - Method in class bioroot.DBUtil

Looks for a particular name in a table with a Name column.

isNameUnique(String, String, int) - Method in class bioroot.DBUtil

Looks for a particular name in a table with a Name column and a particular lab group.

isNameUnique(String, String) - Method in class util.gen.SQL

Looks for a particular name in a table with a Name column.

isNotEmpty(String) - Static method in class util.gen.Misc

Method to check if a string is not null and contains more than "".

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

isOligoNameUnique(DBUtil) - Method in class bioroot.oligo.OligoBean

checks to see if oligo name is unique within labgroup, assumes a connection has been made

isOrdered() - Method in class bioroot.Preference

isPasswordReset() - Method in class bioroot.UserRegistrationBean

isPhaseSet() - Method in class util.bio.parsers.gff.Gff3Feature

isPlasmidNameUnique(DBUtil) - Method in class bioroot.plasmid.PlasmidBean

checks to see if plasmid name is unique within labgroup, assumes a connection has been made

isPrintMe() - Method in class util.bio.xamer.Xamer

isProteinVis() - Method in class gata.main.GATAParams

isQuantileNormalizeAll() - Method in class trans.main.T2Parameter

isRNAVis() - Method in class gata.main.GATAParams

isReagentNameUnique(DBUtil, String) - Method in class bioroot.ReagentBean

checks to see if oligo name is unique within labgroup, assumes a connection has been made

isSavePngs() - Method in class trans.graphics.RankedSetAnalysis

isScaleBarVis() - Method in class gata.main.AnnoSpecParams

isScaleRulerVis() - Method in class gata.main.AnnoSpecParams

isScoreSet() - Method in class util.bio.parsers.gff.Gff3Feature

isSenseStrand() - Method in class trans.roc.Positive

isStartSet() - Method in class util.bio.parsers.gff.Gff3Feature

isStrainNameUnique(DBUtil) - Method in class bioroot.strain.StrainBean

checks to see if strain name is unique within labgroup, assumes a connection has been made

isStringEmpty(String) - Static method in class gata.main.GATAUtil

isStringEmpty(String) - Static method in class util.gen.Misc

Returns true if a String contains just white space or is empty.

isSuperUser() - Method in class bioroot.UserBean

isTiesFound() - Method in class util.gen.RankedFloatArray

isTranslationFlag() - Method in class util.bio.annotation.GeneRep

isTreatmentReplica() - Method in class trans.main.ChromSet

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

Indicates if there are more results to the list.

isUseMMData() - Method in class trans.cel.QuantileNormalization

isUsePseudoMedian() - Method in class trans.main.T2Parameter

isUseRandomPermutation() - Method in class trans.main.T2Parameter

isUseSymmetricNull() - Method in class trans.main.T2Parameter

isValid() - Method in class util.bio.parsers.gff.Gff3Feature

Call to find out if the unparsed GFF line correctly parsed.

isVisible() - Method in class bioroot.Feature

isVisible() - Method in class bioroot.TableHeading