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A
ADFDataBaseSplitter
- class util.bio.parsers.
ADFDataBaseSplitter
.
ADFDataBaseSplitter()
- Constructor for class util.bio.parsers.
ADFDataBaseSplitter
ALToLine2DArray(ArrayList)
- Static method in class gata.main.
GATAUtil
ALToString(ArrayList)
- Static method in class gata.main.
GATAUtil
ALToString(ArrayList)
- Static method in class util.bio.annotation.
GeneGroup
AWSAuthConnection
- class com.amazon.s3.
AWSAuthConnection
.
An interface into the S3 system.
AWSAuthConnection(String, String)
- Constructor for class com.amazon.s3.
AWSAuthConnection
AWSAuthConnection(String, String, boolean)
- Constructor for class com.amazon.s3.
AWSAuthConnection
AWSAuthConnection(String, String, boolean, String)
- Constructor for class com.amazon.s3.
AWSAuthConnection
AWSAuthConnection(String, String, boolean, String, int)
- Constructor for class com.amazon.s3.
AWSAuthConnection
Create a new interface to interact with S3 with the given credential and connection parameters
AWS_ACCESS_KEY_PROPERTY_NAME
- Static variable in class util.amazon.
S3CodeSamples
AWS_SECRET_KEY_PROPERTY_NAME
- Static variable in class util.amazon.
S3CodeSamples
AccountManagement
- class bioroot.
AccountManagement
.
AccountManagement()
- Constructor for class bioroot.
AccountManagement
AggregatePlots
- class trans.graphics.
AggregatePlots
.
For each region finds the underlying scores from the chromosome specific bar files.
AggregatePlots(String[])
- Constructor for class trans.graphics.
AggregatePlots
AlignPanel
- class gata.plotter.
AlignPanel
.
AlignPanel(GATAParams)
- Constructor for class gata.plotter.
AlignPanel
AlignParams
- class gata.aligner.
AlignParams
.
AlignParams()
- Constructor for class gata.aligner.
AlignParams
AlignParams(AlignerPreferences)
- Constructor for class gata.aligner.
AlignParams
AlignedBaseCounter
- class util.bio.converters.
AlignedBaseCounter
.
Counts and parses the bases in a multiple alignment where each string is broken into three sections like gatcc GGCCAATT cgatcca, ccat GGCCAATT cctttt, like the output from meme the central portion is aligned, the left and right flanks are not.
AlignedBaseCounter()
- Constructor for class util.bio.converters.
AlignedBaseCounter
AlignerInputForm
- class gata.aligner.
AlignerInputForm
.
AlignerInputForm(GATAligner)
- Constructor for class gata.aligner.
AlignerInputForm
AlignerInputPanel
- class gata.aligner.
AlignerInputPanel
.
AlignerInputPanel(JFrame, GATAligner)
- Constructor for class gata.aligner.
AlignerInputPanel
Complex class containing most everything to show and process the GATAligner inputs.
AlignerPreferences
- class gata.aligner.
AlignerPreferences
.
AlignerPreferences()
- Constructor for class gata.aligner.
AlignerPreferences
AlignerThread
- class gata.aligner.
AlignerThread
.
AlignerThread(ProgressMonitor, AlignerInputForm)
- Constructor for class gata.aligner.
AlignerThread
Alignment
- class gata.aligner.
Alignment
.
Alignment(String, int, int, String, int, int, int, int, AlignParams, LocalAlignment)
- Constructor for class gata.aligner.
Alignment
Alignment
- class util.bio.calc.
Alignment
.
Methods associated with alignments, pvalues, blast.
Alignment()
- Constructor for class util.bio.calc.
Alignment
AnnoSpecParams
- class gata.main.
AnnoSpecParams
.
AnnoSpecParams()
- Constructor for class gata.main.
AnnoSpecParams
AnnotateRegions
- class trans.anno.
AnnotateRegions
.
For annotating Intervals or binding regions with gene information, proximity, neighbors, and bias based on random trials.
AnnotateRegions(String[])
- Constructor for class trans.anno.
AnnotateRegions
AnnotateRegionsWithGeneList
- class trans.anno.
AnnotateRegionsWithGeneList
.
For annotating a picks file (chr, start, stop) with gene information for a particular list of CG names.
AnnotateRegionsWithGeneList(String[])
- Constructor for class trans.anno.
AnnotateRegionsWithGeneList
Annotation
- class gata.geneGlyphs.
Annotation
.
Annotation(AnnoSpecParams, GATAParams)
- Constructor for class gata.geneGlyphs.
Annotation
AntibodyBase
- class bioroot.antibody.
AntibodyBase
.
AntibodyBase()
- Constructor for class bioroot.antibody.
AntibodyBase
AntibodyBean
- class bioroot.antibody.
AntibodyBean
.
AntibodyBean()
- Constructor for class bioroot.antibody.
AntibodyBean
AntibodyBean(ResultSet)
- Constructor for class bioroot.antibody.
AntibodyBean
AntibodyBean(int, DBUtil)
- Constructor for class bioroot.antibody.
AntibodyBean
Assumes id is not zero
AntibodyModify
- class bioroot.antibody.
AntibodyModify
.
Servlet to modify antibodys using antibodyBeans referenced from a Session object.
AntibodyModify()
- Constructor for class bioroot.antibody.
AntibodyModify
AntibodyPrep
- class bioroot.antibody.
AntibodyPrep
.
AntibodyPrep(int, ResultSet)
- Constructor for class bioroot.antibody.
AntibodyPrep
AntibodyPrep()
- Constructor for class bioroot.antibody.
AntibodyPrep
AntibodySpreadSheet
- class bioroot.antibody.
AntibodySpreadSheet
.
AntibodySpreadSheet()
- Constructor for class bioroot.antibody.
AntibodySpreadSheet
AntibodyViewPreferences
- class bioroot.antibody.
AntibodyViewPreferences
.
AntibodyViewPreferences()
- Constructor for class bioroot.antibody.
AntibodyViewPreferences
Archive
- class bioroot.
Archive
.
Archive()
- Constructor for class bioroot.
Archive
ArrayPrinter
- class util.apps.
ArrayPrinter
.
Prints serialized arrays to screen.
ArrayPrinter()
- Constructor for class util.apps.
ArrayPrinter
AverageACels
- class trans.cel.
AverageACels
.
Averages two serialized float[][]s, like xxx.cela files, from the CelFileConverter app.
AverageACels()
- Constructor for class trans.cel.
AverageACels
AverageDoubles
- class trans.misc.
AverageDoubles
.
Slides a 50 index window along an array averaging the contents.
AverageDoubles()
- Constructor for class trans.misc.
AverageDoubles
AveragePCels
- class trans.cel.
AveragePCels
.
Averages serialized float[]s, like xxx.celp files, from the CelProcessor app.
AveragePCels()
- Constructor for class trans.cel.
AveragePCels
actionPerformed(ActionEvent)
- Method in class gata.aligner.
BrowseButtonAction
actionPerformed(ActionEvent)
- Method in class gata.menu.
SaveImagePanel
add(int, float)
- Method in class trans.main.
WindowBlockMakerTwoColor
Adds a gr line to the global ArrayLists for later burning to bar.
addAction(JButton, int)
- Method in class gata.plotter.
ToolsFrame
addAnAntibodyPrep(AntibodyBean, DBUtil)
- Static method in class bioroot.antibody.
NewAntibody
Adds a new antibodyPrep to the AntibodyBean
addBlankLines(AntibodyBean, String[], int)
- Static method in class bioroot.antibody.
AntibodySpreadSheet
Adds "" to items base on the number of preps and uses in the antibody bean.
addExpectedSubSeq(int)
- Method in class selex.
SelexParams
addFlashCard(Flash.FlashCard)
- Method in class util.apps.
Flash
Adds flash card to the end of the array.
addHeatMapBlocks(int, int)
- Method in class trans.main.
WindowBlockMakerTwoColor
Make a heatmap blocks from given window indexes, stop not included.
addIt()
- Method in class trans.main.
IntervalMaker
addIt()
- Method in class trans.main.
MultiWindowIntervalMaker
addIt()
- Method in class trans.main.
SetNumberIntervalMaker
addLabel(ArrayList)
- Method in class gata.main.
AnnoSpecParams
addNormalDNALines(ArrayList)
- Method in class gata.main.
AnnoSpecParams
addObsExpRatio(double)
- Method in class selex.
SelexParams
addObservedSubSeq(int)
- Method in class selex.
SelexParams
addOldUserAttributes()
- Method in class bioroot.
UserRegistrationBean
addParent(StrainBean, HashMap, DBUtil, UserBean)
- Static method in class bioroot.strain.
NewStrain
addPermutatedScoresToHistogram(ArrayList)
- Method in class trans.main.
ScanChip
Uses random permutation of the cel file labels to estimate a null distribution, store random scores in a histogram for p-value and FDR estimations.
addPermutatedScoresToHistogram(ArrayList)
- Method in class trans.main.
ScanChromosomes
Uses random permutation of the cel file labels to estimate a null distribution, store random scores in a histogram for p-value and FDR estimations.
addPlasmid(AntibodyBean, HashMap, DBUtil, UserBean)
- Static method in class bioroot.antibody.
AntibodyBase
addPlasmid(StrainBean, HashMap, DBUtil, UserBean)
- Static method in class bioroot.strain.
NewStrain
addProteinLines(ArrayList, ArrayList)
- Method in class gata.main.
AnnoSpecParams
addRNALines(Line2D.Double, ArrayList)
- Method in class gata.main.
AnnoSpecParams
addScaleRuler(JMenu, String)
- Method in class gata.menu.
GATAFrame
addScaleTrackColors(JMenu)
- Method in class gata.menu.
GATAFrame
addShowHide(JMenu, String, boolean)
- Method in class gata.menu.
GATAFrame
addShowHideLabel(JMenu, String)
- Method in class gata.menu.
GATAFrame
addShowHideWithPath(JMenu, String, String)
- Method in class gata.menu.
GATAFrame
addStrain(AntibodyBean, HashMap, DBUtil, UserBean)
- Static method in class bioroot.antibody.
AntibodyBase
addStrain(PlasmidBean, HashMap, int, DBUtil)
- Static method in class bioroot.plasmid.
NewPlasmid
addThinDNALines(ArrayList)
- Method in class gata.main.
AnnoSpecParams
addTrack(JMenu, String, boolean)
- Method in class gata.menu.
GATAFrame
addUseDilution(AntibodyBean, DBUtil, int)
- Static method in class bioroot.antibody.
NewAntibody
Adds a new UseDilution to the indicated AntibodyPrep
addUseDilutionBlankLines(boolean, String[], AntibodyPrep, int, DBUtil)
- Static method in class bioroot.antibody.
AntibodySpreadSheet
Adds "" to items based on the number of use dilutions present in the Antibody Prep bean.
addZeros(String)
- Static method in class util.gen.
Misc
Prepends zeros to a string such that its total length = 10.
addZeros(String[])
- Static method in class util.gen.
Misc
Prepends zeros to each String such that its total length = 10.
all4BaseCombinations
- Static variable in class util.bio.seq.
Seq
All possible 4 base combinations.
antiLog(double, int)
- Static method in class util.gen.
Num
Converts to unlogged value.
antiLog(float[], int)
- Static method in class util.gen.
Num
Converts an array float[] to unlogged values.
antibodyPrepFeatureNames
- Static variable in class bioroot.antibody.
AntibodyBase
Used to see if any antibody preps are called for spreadsheet.
anyNaNs(IntensityFeature[])
- Static method in class trans.cel.
CelProcessor
Looks for NaN in IntensityFeatures.
anyNaNs(float[])
- Static method in class trans.cel.
CelProcessor
Looks for NaN in IntensityFeatures.
ap
- Variable in class gata.aligner.
Blast
append(String)
- Method in class util.gen.
TextFrame
appendDouble(double[], double)
- Static method in class util.gen.
Num
Returns a new array with the newValue appended on the end.
appendLength(int)
- Method in class selex.
SelexParams
appendMemeParserReport(String)
- Method in class meme.
MemeResults
appendMemeReports(String)
- Method in class meme.
MemeResults
appendMessages(String)
- Method in class bioroot.
ReagentBean
appendMotifSearchResults(String)
- Method in class meme.
MemeResults
appendMummerHits()
- Method in class trans.tpmap.
MummerMapper
Runs through mummer results and appends any hits to filtered1lq
appendNotes(String)
- Method in class trans.qc.
CelFileStats
appendPlasmidBeans(HttpSession, PlasmidBean[])
- Static method in class bioroot.plasmid.
PlasmidUpload
Sets plasmidBeans attribute by appending any new beans to the beginning.
appendSelexOligoFiles(String)
- Method in class meme.
MemeResults
appendStrainBeans(HttpSession, StrainBean[])
- Static method in class bioroot.strain.
StrainUpload
Sets strainBeans attribute by appending any new beans to the beginning.
appendSub(String)
- Method in class selex.
SelexParams
areGenericLabelsVis()
- Method in class gata.main.
GATAParams
areLabelsVis()
- Method in class gata.main.
GATAParams
arrayList2IntArrayArray(ArrayList)
- Static method in class util.gen.
Num
Converts an ArrayList of int[]s to int[][].
arrayListOfDoubleToArray(ArrayList)
- Static method in class util.gen.
Num
ArrayList of Double to double[]
arrayListOfFloatToArray(ArrayList)
- Static method in class util.gen.
Num
ArrayList of Float to float[]
arrayListToArray(ArrayList)
- Static method in class bioroot.
PatternMatch
Convert an ArrayList of PatternMatch to PatternMatch[]
arrayListToDoubles(ArrayList)
- Static method in class util.gen.
Num
ArrayList of Double to double[]
arrayListToInts(ArrayList)
- Static method in class util.gen.
Num
ArrayList of Integer to int[]
assembleHeatMapBlocks()
- Method in class trans.main.
WindowBlockMakerTwoColor
assignGenericFeatureTracks()
- Method in class gata.geneGlyphs.
Annotation
assignPValues()
- Method in class expr.
CorrelationMaps
Assigns right tail -10Log10(pvalues) for each score > 0 in the CorrelationWindows
aveFoldDiffCombine(int[], int[])
- Static method in class util.gen.
Num
Calculates the average fold difference between two int[]s of the same length.
aveFoldDiffIndividual(int[], int[])
- Static method in class util.gen.
Num
Calculates the average fold difference between two int[]s of the same length.
aveMedianAbsDiffSubWinControl(Interval)
- Static method in class trans.main.
IntervalReportPrinter
Calculate maximum median absolute diff of SubWindow control values
averageDoubleArrayList(ArrayList)
- Static method in class selex.
UtilSelex
Averages an ArrayList of Double objects.
averageFloatArray(float[])
- Static method in class util.gen.
Num
Averages a float[]
averageFloatArrays(float[][])
- Static method in class util.gen.
Num
Average float[][] values to double[], averages repeats [values][numRepeats]
averageFloatArraysFlipped(float[][])
- Static method in class util.gen.
Num
Average float[][] values to double[], averages repeats [numChips][OligoValues].
averageFloatArraysFlippedToFloat(float[][])
- Static method in class util.gen.
Num
Average float[][] values to double[], averages repeats [numChips][OligoValues].
averageFloatArraysFlippedToFloats(float[][])
- Static method in class util.gen.
Num
Average float[][] values to float[], averages repeats [numChips][OligoValues].
averageIntArray(int[])
- Static method in class util.gen.
Num
Averages a int[]
averageIntIntArray(int[][])
- Static method in class util.gen.
Num
Average int[][] values to double[], averages repeats [numRepeats][values]
averageIntIntArray2(int[][])
- Static method in class util.gen.
Num
Average int[][] values to double[], averages values [numRepeats][values]
averageIntegerArrayList(ArrayList)
- Static method in class selex.
UtilSelex
Averages an ArrayList of Integer objects.
averageWindowScores(int, int)
- Method in class trans.main.
PeakPicker
Averages the smoothed oligo scores, stop is inclusive.
awsCredentials
- Variable in class util.amazon.
S3Manager
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