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

P

PMMMTransformer - class nix.affy.main.PMMMTransformer.

Performs a max(PM-MM,0) transformation on serialized float[]s.

PMMMTransformer() - Constructor for class nix.affy.main.PMMMTransformer

PWMScoreWindows - class nix.affy.roc.PWMScoreWindows.

Scores windows for hits to a transcription factor PWM, for RocWindow filtering.

PWMScoreWindows(String[]) - Constructor for class nix.affy.roc.PWMScoreWindows

ParsePatternedWindows - class nix.affy.roc.ParsePatternedWindows.

Finds RocWindows upstream and withing the neighborhood of the ATG start site of a patterned gene list.

ParsePatternedWindows(String[]) - Constructor for class nix.affy.roc.ParsePatternedWindows

ParseSgrsForParticularRegions - class nix.affy.roc.ParseSgrsForParticularRegions.

Returns oligo values that overlap particular regions.

ParseSgrsForParticularRegions(String[]) - Constructor for class nix.affy.roc.ParseSgrsForParticularRegions

Passwords - class nix.util.gen.Passwords.

Methods for generating one time passwords.

Passwords() - Constructor for class nix.util.gen.Passwords

PatternMatch - class nix.bdtnp.bid.PatternMatch.

Class to hold information and helper methods relating to pattern matches.

PatternMatch(int, int, String) - Constructor for class nix.bdtnp.bid.PatternMatch

PeakPicker - class nix.affy.main.PeakPicker.

Finds peaks in Intervals.

PeakPicker() - Constructor for class nix.affy.main.PeakPicker

PlotterPreferences - class nix.gata.main.PlotterPreferences.

PlotterPreferences() - Constructor for class nix.gata.main.PlotterPreferences

PosRegion - class nix.affy.main.PosRegion.

For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval.

PosRegion(String, String, int, int) - Constructor for class nix.affy.main.PosRegion

Positive - class nix.affy.roc.Positive.

Container for a positive BAC used by the Sgr scripts.

Positive(String, int, int) - Constructor for class nix.affy.roc.Positive

PossumToGFF - class nix.util.bio.converters.PossumToGFF.

Converts a copied Possum output to GFF annotation, prints to screen, sorted by score.

PossumToGFF() - Constructor for class nix.util.bio.converters.PossumToGFF

Probe - class nix.bdtnp.bid.Probe.

Class to process the Probe.jsp and create a ProbeBean

Probe() - Constructor for class nix.bdtnp.bid.Probe

ProbeBean - class nix.bdtnp.bid.ProbeBean.

Bean to hold info related to a Probe which is used in a Stain.

ProbeBean() - Constructor for class nix.bdtnp.bid.ProbeBean

ProbeBean(int, BIDUtil, BIDUtil) - Constructor for class nix.bdtnp.bid.ProbeBean

ProbeBean(int, BIDUtil) - Constructor for class nix.bdtnp.bid.ProbeBean

paintComponent(Graphics) - Method in class nix.affy.graphics.DrawPanel

paintComponent(Graphics) - Method in class nix.affy.graphics.VirtualCelPanel

paintComponent(Graphics) - Method in class nix.gata.geneGlyphs.GlyphPanel

Watch order of drawing, optimize to avoid changing stroke

paintComponent(Graphics) - Method in class nix.gata.plotter.AlignPanel

paintComponent(Graphics) - Method in class nix.util.apps.ScatterDrawPanel

parseBl2SeqResults(String[]) - Method in class nix.util.bio.wrappers.BL2Seq

This takes an array of BLAST bl2seq results and parses the info into an array

parseBlast(String[]) - Method in class nix.gata.aligner.Blast

parseBlast(String[]) - Static method in class nix.util.bio.wrappers.SimpleBlast

parseBlastGeneral(String[]) - Static method in class nix.util.bio.wrappers.SimpleBlast

Parses blast output from blastall for dna into BlastResult objects.

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

parseInt(String, int) - Static method in class nix.util.gen.Num

Attemps to parse an int, returns failNumber if it fails.

parseIntervalFile(File, int) - Static method in class nix.affy.anno.AnnotateRegions

Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window.

parseIntervalFile(File, int) - Static method in class nix.affy.anno.AnnotateRegionsWithGeneList

Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window.

parseIt(File) - Method in class nix.util.bio.parsers.MultiFastaParser

parseIt(File) - Method in class nix.util.bio.parsers.gff.Gff3Parser

parseLine(String, Pattern) - Static method in class nix.gata.aligner.Blast

parseLine(String, Pattern) - Static method in class nix.util.bio.wrappers.BL2Seq

parseLine(String, Pattern) - Static method in class nix.util.bio.wrappers.SimpleBlast

parseMemeText(String[]) - Method in class nix.meme.MemeParser

parseMultiPartRequest(HttpServletRequest) - Static method in class nix.util.gen.HTML

Parses a multipart request returning a HashMap of fieldName: String, if the same fieldName is found more than once, a String[] is created.

parsePicksFile(File, int) - Static method in class nix.affy.anno.AnnotateRegions

parsePicksFile(File, int) - Static method in class nix.affy.anno.AnnotateRegionsWithGeneList

parseRegionFile(File) - Static method in class nix.affy.roc.ParseSgrsForParticularRegions

parseRegions(File) - Static method in class nix.affy.anno.IntersectIntervalsWithRegions

Parses a file for a tab delimited list of at minimum, chrom, start, stop, (optional) notes into a Region[].

parseStringArray(Object) - Static method in class nix.util.gen.HTML

For extracting either a String[] or making a new String[] by casting the object as a String.

parseStringToDouble(String) - Static method in class nix.util.bio.parsers.gff.GffFeature

pathToJava - Static variable in class nix.util.gen.JQsub

pentamerGenerator() - Static method in class nix.util.bio.xamer.XamerCounter

percent(int, int) - Static method in class nix.affy.main.OverlapCounter

pickPeaks(Interval[]) - Method in class nix.affy.main.PeakPicker

plotHistogram() - Method in class nix.selex.SelexParams

populateBean(Object, HttpServletRequest) - Static method in class nix.util.gen.HTML

Fills in all the params of a bean.

positive(Positive[], Sgr) - Static method in class nix.affy.roc.SgrBacCounter

Checks to see if an sgr object is one of the positives.

postMail(String[], String, String, String) - Method in class nix.util.gen.Email

postMailNoAuthentication(String[], String, String, String, String, String) - Static method in class nix.util.gen.Email

Simple static method for sending email, no authentication, modified from http://www.javacommerce.com/articles/sendingmail.htm Sudhir Ancha.

postWithAttachment(String[], String, String, String, String, String) - Method in class nix.util.gen.Email

print() - Method in class nix.util.gen.Histogram

printAlignment() - Method in class nix.gata.aligner.Alignment

printArray(Object[]) - Static method in class nix.util.gen.Misc

Prints a Object[] to System.out

printArray(String[]) - Static method in class nix.util.gen.Misc

Prints a String[] to System.out

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

Prints ArrayList to System.out

printArray(int[]) - Static method in class nix.util.gen.Misc

Prints a int[] to System.out

printArray(float[]) - Static method in class nix.util.gen.Misc

Prints a int[] to System.out

printArray(double[]) - Static method in class nix.util.gen.Misc

Prints a int[] to System.out

printArray(double[][]) - Static method in class nix.util.gen.Misc

Print to System.out a double[][]

printArray(float[][]) - Static method in class nix.util.gen.Misc

Print to System.out a float[][]

printArray(int[][]) - Static method in class nix.util.gen.Misc

Print to System.out a int[][]

printCalculations(ArrayList, int) - Static method in class nix.affy.misc.CalcGCAndTransform

Prints %GC, Mean, 3xStdErr

printCalculations(ArrayList, int) - Static method in class nix.affy.misc.CalcGCRatiosFromIntervals

Prints %GC, Mean, 3xStdErr

printChroms(RocWindow[]) - Static method in class nix.affy.roc.ParsePatternedWindows

printDistToClosestATGAndTranscript(BindingRegion[]) - Method in class nix.affy.anno.AnnotateRegions

Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.

printDistToClosestATGAndTranscript(BindingRegion[]) - Method in class nix.affy.anno.AnnotateRegionsWithGeneList

Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.

printDoc() - Static method in class nix.selex.UtilSelex

printDocs() - Static method in class nix.affy.anno.AnnotateRegions

printDocs() - Static method in class nix.affy.anno.AnnotateRegionsWithGeneList

printDocs() - Static method in class nix.affy.anno.IntersectIntervalsWithRegions

printDocs() - Static method in class nix.affy.bpmap.BPMapOligoBlastFilter

printDocs() - Static method in class nix.affy.bpmap.BPMapProcessor

printDocs() - Static method in class nix.affy.bpmap.BPMapSort

printDocs() - Static method in class nix.affy.bpmap.MummerFilter

printDocs() - Static method in class nix.affy.graphics.CelMasker

printDocs() - Static method in class nix.affy.graphics.IntervalPlotter

printDocs() - Static method in class nix.affy.graphics.VirtualCel

printDocs() - Static method in class nix.affy.main.BindingRegionGraphPrinter

printDocs() - Static method in class nix.affy.main.CelMapper

printDocs() - Static method in class nix.affy.main.CelProcessor

printDocs() - Static method in class nix.affy.main.FindSubBindingRegions

printDocs() - Static method in class nix.affy.main.IntensityPrinter

printDocs() - Static method in class nix.affy.main.IntervalFilter

printDocs() - Static method in class nix.affy.main.IntervalGFFPrinter

printDocs() - Static method in class nix.affy.main.IntervalGraphPrinter

printDocs() - Static method in class nix.affy.main.IntervalMaker

printDocs() - Static method in class nix.affy.main.IntervalReportPrinter

printDocs() - Static method in class nix.affy.main.LoadIntervalOligoInfo

printDocs() - Static method in class nix.affy.main.OligoIntensityPrinter

printDocs() - Static method in class nix.affy.main.OverlapCounter

printDocs() - Static method in class nix.affy.main.RatioTest

printDocs() - Static method in class nix.affy.main.ScoreIntervals

printDocs() - Static method in class nix.affy.main.SkepticalSumIntensityTest

printDocs() - Static method in class nix.affy.main.SumIntensityTest

printDocs() - Static method in class nix.affy.main.WindowScanner

printDocs() - Static method in class nix.affy.roc.PWMScoreWindows

printDocs() - Static method in class nix.affy.roc.ParsePatternedWindows

printDocs() - Static method in class nix.meme.UtilMeme

printDocs() - Static method in class nix.util.apps.FileJoiner

printDocs() - Static method in class nix.util.apps.FileSplitter

printDocs() - Static method in class nix.util.apps.FileTrimmer

printDocs() - Static method in class nix.util.apps.ScatterPlot

printDocs() - Static method in class nix.util.apps.ScoreChromosomes

printDocs() - Static method in class nix.util.apps.ScoreSequences

printEnz() - Method in class nix.util.bio.digest.Enzyme

printGFF() - Method in class nix.affy.main.IntervalGFFPrinter

printHashSetToFile(HashSet, String) - Static method in class nix.util.gen.Misc

Prints a HashSet to a file.

printHistogram(int[]) - Static method in class nix.util.gen.Histogram

Prints a simple histogram.

printHistogram(int[], String[]) - Static method in class nix.util.gen.Histogram

Prints a simple histogram.

printHistogram(int[], PrintWriter) - Static method in class nix.util.gen.Histogram

Prints a simple histogram to a PrintWriter.

printLocalAlignment() - Method in class nix.gata.aligner.LocalAlignment

printMFP() - Method in class nix.util.bio.parsers.MultiFastaParser

printMFP() - Method in class nix.util.bio.parsers.QualityFileParser

printMapCelFiles(File) - Method in class nix.affy.main.CelMapper

Method for maping a cel file to a bpmap method and printing a tab delimited text file.

printNotes() - Method in class nix.util.bio.parsers.gff.Gff3Parser

printQuantiles() - Method in class nix.affy.main.QuantileNormalization

Prints Quantile arrays to System.out using toString().

printReport() - Method in class nix.affy.main.IntervalReportPrinter

printReport() - Method in class nix.util.bio.parsers.MultiFastaParser

printReport() - Method in class nix.util.bio.parsers.QualityFileParser

printSGRWindows(RocWindow[]) - Static method in class nix.affy.roc.RocWindow

printSave(String) - Method in class nix.meme.MemeResults

printSave(String) - Method in class nix.selex.SelexParams

printSaveIntervalScoreGraphFiles() - Method in class nix.affy.main.IntervalGraphPrinter

Prints and saves a Affy .sgr file

printScores(Interval[], File, boolean) - Static method in class nix.affy.main.IntervalGraphPrinter

Prints to a File a line for every Oligo in each Interval.

printSeqFiles() - Method in class nix.selex.SeqFiles

printSeqRead() - Method in class nix.selex.SeqRead

printSeqsToConsole() - Method in class nix.gata.plotter.ConservedSeqs

printStringArray(String[], String) - Static method in class nix.util.bio.converters.RepeatMaskerToGFF

Prints out the string array on a line divided by the separator, good for debugging

printSubSeq() - Method in class nix.selex.SubSeq

printToTextArea(String) - Method in class nix.gata.plotter.Console

printTruncatedSeqsToConsole(int, int, int, int) - Method in class nix.gata.plotter.ConservedSeqs

processArgs(String[]) - Method in class nix.affy.anno.AnnotateRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.anno.AnnotateRegionsWithGeneList

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.anno.IntersectIntervalsWithRegions

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.bpmap.BPMapOligoBlastFilter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.bpmap.BPMapProcessor

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.bpmap.BPMapSort

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.bpmap.MummerFilter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.graphics.CelMasker

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.graphics.IntervalPlotter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.graphics.VirtualCel

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.BindingRegionGraphPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.CelMapper

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.CelProcessor

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.FindSubBindingRegions

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.main.IntensityPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.IntervalFilter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.IntervalGFFPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.IntervalGraphPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.IntervalMaker

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.main.IntervalReportPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.LoadIntervalOligoInfo

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.main.OligoIntensityPrinter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.OverlapCounter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.RatioTest

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.main.ScoreIntervals

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.affy.main.SkepticalSumIntensityTest

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.main.SumIntensityTest

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.main.WindowScanner

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.roc.PWMScoreWindows

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.affy.roc.ParsePatternedWindows

This method will process each argument and assign new varibles

processArgs(String[]) - Method in class nix.selex.SelexParams

processArgs(String[]) - Method in class nix.util.apps.FileJoiner

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.util.apps.FileSplitter

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.util.apps.FileTrimmer

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.util.apps.ScoreChromosomes

This method will process each argument and assign any new varibles

processArgs(String[]) - Method in class nix.util.apps.ScoreSequences

This method will process each argument and assign any new varibles

processLocalAlignment() - Method in class nix.gata.aligner.LocalAlignment