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

F

FDRVsQValues - class trans.main.FDRVsQValues.

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

FDRWindowConverter - class trans.main.FDRWindowConverter.

Associates an empirical FDR estimate with each window provided a mock IP was performed.

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

Feature - class bioroot.Feature.

Feature(String) - Constructor for class bioroot.Feature

FetchGenomicSequences - class util.bio.parsers.FetchGenomicSequences.

Fetches the genomic sequences for a list of regions.

FetchGenomicSequences(String[]) - Constructor for class util.bio.parsers.FetchGenomicSequences

FetchIndexedSequence - class util.bio.seq.FetchIndexedSequence.

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

FileFocusListener - class gata.aligner.FileFocusListener.

FileFocusListener() - Constructor for class gata.aligner.FileFocusListener

FileInputForm - class gata.menu.FileInputForm.

FileInputForm(GATAParams) - Constructor for class gata.menu.FileInputForm

FileInputPanel - class gata.menu.FileInputPanel.

FileInputPanel(GATAParams, JFrame) - Constructor for class gata.menu.FileInputPanel

FileJoiner - class util.apps.FileJoiner.

Joins text files into a single file, avoiding line concatenations.

FileJoiner(String[]) - Constructor for class util.apps.FileJoiner

FileSize - class util.gen.FileSize.

FileSize(File) - Constructor for class util.gen.FileSize

FileSplitter - class util.apps.FileSplitter.

Application for splitting a large text file into smaller files given a maximum number of lines.

FileSplitter(String[]) - Constructor for class util.apps.FileSplitter

FileTrimmer - class util.apps.FileTrimmer.

Removes empty lines from text files in a given directory.

FileTrimmer(String[]) - Constructor for class util.apps.FileTrimmer

FilterTPMapByRegions - class trans.tpmap.FilterTPMapByRegions.

Filters a TPMap file by regions (tab delimited: chr start stop).

FilterTPMapByRegions(String[]) - Constructor for class trans.tpmap.FilterTPMapByRegions

FindSubBindingRegions - class trans.main.FindSubBindingRegions.

Finds the best sub window and binding peaks (using the PeakPicker) within each interval.

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

Flash - class util.apps.Flash.

Flash(String[]) - Constructor for class util.apps.Flash

factorial(int) - Static method in class util.gen.Num

Calculates N! modified from http://www.unix.org.ua/orelly/java-ent/jnut/ch01_03.htm

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

Prints message to screen, to log4j error, then exits.

fetchAllFilesRecursively(File) - Static method in class util.gen.IO

Fetches all files in a directory recursing through sub directories.

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

Fetches all files with a given extension in a directory recursing through sub directories.

fetchAllS3ObjectKeyNames() - Method in class util.amazon.S3Manager

Fetches the key names of the S3 objects.

fetchAndAssignGATAParams(GATAParams) - Method in class gata.main.PlotterPreferences

fetchAntibodyBeans(String, DBUtil) - Static method in class bioroot.antibody.AntibodySpreadSheet

Build AntibodyBean[] from Antibody table in database.

fetchAntibodyTableRows(UserBean, AntibodyBean[], int[], DBUtil, boolean, boolean) - Static method in class bioroot.antibody.AntibodySpreadSheet

Returns table rows for every oligo according to a Preference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.

fetchArrayList(File) - Static method in class gata.main.GATAUtil

fetchArrayList(File) - Static method in class util.gen.IO

Fetches an ArrayList stored as a serialize object file.

fetchArrowButton(String, String, String, int) - Static method in class util.gen.HTML

Returns an upDown arrow ala Mac look and feel that will set a formParm to a given value and submit the form provided the form is named "form" (ie

fetchBLASTParams(int, int) - Static method in class gata.main.GATAUtil

Returns Lambda and K or null for a given match and misMatch from BLASTN.

fetchBLASTParams(int, int) - Static method in class util.bio.calc.Alignment

Returns Lambda, K, H or null for a given match and misMatch from BLASTN.

fetchBoolean(String) - Method in class trans.main.T2Parameter

fetchBottomCenterY(Cluster) - Method in class util.bio.cluster.ClusterDrawPanel

Recurse through clusters always going lower to find center

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

fetchCellTypeConcats(int, UserBean) - Method in class bioroot.DBUtil

Fetches concatinate of name and notes from CellType

fetchCenteredFowardAndReverseCounts() - Method in class util.gen.Histogram

Returns two columns as int[columns][counts] centered on max value with zeros as filler.

fetchCheckBoxNumberTableRows(Feature[], int) - Static method in class bioroot.Feature

fetchCheckGroup(String, String, String[]) - Static method in class util.gen.HTML

Returns a selected check box group with the toSelect selected if present in the String[]

fetchChromosomeFiles(File[], String) - Static method in class trans.cel.MakeChromosomeSets

Extracts all the Files with a given chromosome name from a list of directories

fetchChromosomeSpecificBRs(BindingRegion[], String) - Static method in class trans.anno.IntersectRegions

Given a sorted array of BindingRegion and a chromosome, returns the appropriate BindingRegions.

fetchClosestOligoScore(Oligo[], int) - Static method in class trans.graphics.IntervalDrawPanel

Finds the closes Oligo to a bp point and returns the indexed score.

fetchClusterCenterY(Cluster) - Method in class util.bio.cluster.ClusterDrawPanel

Returns the 'middle' Y coordinate for the cluster.

fetchColumn(String) - Method in class bioroot.DBUtil

Returns a String[] of the items in a particular column.

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

Returns a concatinate of the results where each String in the String[] represents a results table row where each column entry is separated by the divider String.

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

Returns a concatinate of the results where each String in the String[] represents a results table row where each column entry is separated by the divider String.

fetchConcentrationGroup(OligoBean) - Static method in class bioroot.oligo.OligoBase

Returns a concentration unit

fetchControlIntensities(Quantile[]) - Method in class trans.cel.QuantileNormalization

Uses the control indexes to fetch the control intensities from the Quantile[].

fetchExit(String, HashMap) - Static method in class util.gen.Misc

Looks for key, if not found prints error message and exists.

fetchFalseBlocks(boolean[], int, int) - Static method in class util.bio.annotation.ExportIntergenicRegions

fetchFile(String) - Method in class trans.main.T2Parameter

fetchFiles(PlasmidBean[], StrainBean[], AntibodyBean[], String, DBUtil) - Static method in class bioroot.Archive

Fetches any plasmid or strain files.

fetchFiles(String[], String) - Static method in class util.gen.IO

For each base name (ie /home/data/treat1 ), makes a File object using the chromExtenstion (ie /home/data/treat1.chromExtension ), if it actually exists, it is saved and a File[] returned.

fetchFilesRecursively(File) - Static method in class util.gen.IO

Fetches all files in a directory recursing through sub directories.

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

Fetches all files with a given extension in a directory recursing through sub directories.

fetchFloatArrays(String, boolean) - Static method in class trans.main.ScanChip

Given a directory (or a file), fetches serialized float[] from all files with the .celp extension.

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

Loads float[][]s from disk.

fetchGCContent(Region[]) - Method in class trans.anno.RandomRegions

Converts the Region[] sequences into boolean[]s, everything not g or c are recorded as false.

fetchGCContent(char[]) - Static method in class util.bio.seq.Seq

Converts a DNA sequence into a boolean[], everything not g or c is recorded as false.

fetchGeneConcat(int, UserBean) - Method in class bioroot.DBUtil

Fetches concatinate of name and notes from Gene

fetchGeneNames(int) - Method in class bioroot.DBUtil

Fetches geneNames given a labGroupId, assumes connection to BioRoot+Database.

fetchGoodWindow() - Method in class trans.main.IntervalMaker

fetchGoodWindow() - Method in class trans.main.MultiWindowIntervalMaker

fetchGoodWindow(double) - Method in class trans.main.SetNumberIntervalMaker

fetchHTMLTableRow() - Method in class bioroot.CellTypeBean

fetchHTMLTableRow() - Method in class bioroot.GeneBean

fetchHTMLTableRow() - Method in class bioroot.MarkerBean

fetchHTMLTableRow() - Method in class bioroot.OrganismBean

fetchIdNameMatchArray(String) - Method in class bioroot.DBUtil

Fetches an IndexNameMatch Array.

fetchIntensities(File[], String) - Static method in class trans.main.MultiSGRPrinter

Fetches a float[] from each of the directories given a fileName.

fetchIntensities(File[], String) - Static method in class trans.main.ScanChromosomes

Fetches a float[] from each of the directories given a fileName.

fetchIntensityFeatures(File[]) - Static method in class trans.cel.MakeChromosomeSets

Loads IntensityFeature[]s into a single master.

fetchIntervalLine(Interval, int) - Method in class trans.main.IntervalReportPrinter

fetchIntervalReport(Interval, int) - Method in class trans.main.IntervalReportPrinter

fetchIntrons(ArrayList) - Static method in class gata.main.GATAUtil

Takes an ArrayList of exon startStop int[2]'s, returns an ArrayList of int[2]'s representing the start,stop for each intron

fetchIntrons(boolean[], UCSCGeneLine[]) - Method in class util.bio.annotation.ExportIntronicRegions

fetchIntrons(ArrayList) - Static method in class util.bio.annotation.GeneGroup

Takes an ArrayList of exon startStop int[2]'s, returns an ArrayList of int[2]'s representing the start,stop for each intron

fetchLabGroupName(int) - Method in class bioroot.DBUtil

Fetches an labGroupName given an id, assumes connection to BioRoot+Database.

fetchLabGroups(String[]) - Method in class bioroot.DBUtil

Returns a sorted list of lab groups.

fetchLoadedOligos(File) - Static method in class trans.bkgrnd.CalcBkgrndRatios

fetchLoadedOligos(File) - Static method in class trans.bkgrnd.CalculateBackgroundStats

fetchMarkerConcats(int) - Method in class bioroot.DBUtil

Fetches concatinate of name and notes from Marker

fetchMarkerNames() - Method in class bioroot.DBUtil

Fetches markerNames given an labGroupId, assumes connection to BioRoot+Database.

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

Loose matching of substring guess from larger String[]s.

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

Given a square table and a list of coordinates, will return the associated values.

fetchMaxOligoScore(Oligo[], int, int) - Static method in class trans.graphics.IntervalDrawPanel

Scans oligos for a max score when given a bp range.

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

Calculates the median intensity of a sorted Quantile[].

fetchMinScore(AlignParams[]) - Static method in class gata.plotter.MultiAlignPanel

Finds lowest minScore in an array of AlignParams.

fetchMultipleCells(String) - Method in class bioroot.DBUtil

Returns a String[] of the results.

fetchMultipleCells(String) - Method in class util.gen.SQL

Returns a String[] of the results.

fetchMultipleOptionGroup(String[], String[]) - Static method in class util.gen.HTML

Returns a selected option group with the toSelect selected if present in the String[] of options.

fetchNames() - Method in class bioroot.Preference

returns a String[] of names

fetchNamesAndDirectories(File) - Static method in class util.gen.IO

Given a directory, returns a HashMap of the containing directories' names and a File obj for the directory.

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

fetchNumberedFiles(String, File) - Method in class trans.main.T2Parameter

fetchNumberedOneFile(String, File) - Method in class trans.main.T2Parameter

fetchObject(File) - Static method in class gata.main.GATAUtil

fetchObject(File) - Static method in class util.gen.IO

Fetches an Object stored as a serialized file.

fetchOligoBeans(String, DBUtil) - Static method in class bioroot.oligo.OligoSpreadSheet

Build OligoBean[] from Oligo table in database.

fetchOligoTableRows(Preference, OligoBean[], int[], DBUtil, boolean, boolean) - Static method in class bioroot.oligo.OligoSpreadSheet

Returns table rows for every oligo according to an OligoPreference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.

fetchOptionGroup(String, String[]) - Static method in class util.gen.HTML

Returns a selected option group with the toSelect selected if exactly matches one of the String[] options

fetchOptionGroupLoose(String, String[]) - Static method in class util.gen.HTML

Returns a selected option group with the toSelect selected if at all present in the String[] options.

fetchOrganismConcat(int) - Method in class bioroot.DBUtil

Fetches concatinate of name and notes from Organism

fetchPermutatedArrays() - Method in class trans.main.RandomizeLabels

Attempts to fetch a unique, unseen permutation of the t[][] and control[][] arrays.

fetchPlasmidBeans(String, DBUtil) - Static method in class bioroot.plasmid.PlasmidSpreadSheet

Build PlasmidBean[] from Plasmid table in database.

fetchPlasmidTableRows(UserBean, PlasmidBean[], int[], DBUtil, boolean, boolean) - Static method in class bioroot.plasmid.PlasmidSpreadSheet

Returns table rows for every oligo according to a Preference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.

fetchPossibleValue(String) - Method in class trans.main.T2Parameter

fetchProximalWindows(GeneGroup[], RocWindow[], int) - Static method in class trans.roc.ParsePatternedWindows

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

fetchRadio(String, String, String) - Static method in class util.gen.HTML

Returns a radio input line with CHECKED if the value is equal to the potential

fetchRadioGroup(String, String, String[]) - Static method in class util.gen.HTML

Returns a selected radio group with the toSelect selected if present in the String[]

fetchRadioGroupSubmit(String, String, String[], String) - Static method in class util.gen.HTML

Returns a selected radio group with the toSelect selected if present in the String[] Also throws in a little javascript to submit the form if the button is clicked.

fetchRandomCoordinates(int, int) - Method in class trans.anno.RandomRegions

Given a desired length of sequence, returns multiple random region start stop coordinates.

fetchRandomCoordinates(int, int, double) - Method in class trans.anno.RandomRegions

Given a desired length of sequence, returns multiple random region start stop coordinates.

fetchReaderOnZippedFile(File) - Static method in class util.gen.IO

Returns a BufferedReader from which you can call readLine() directly from a zipped file without decompressing.

fetchReagentCounts(UserBean, String) - Method in class bioroot.DBUtil

Fetches the number of reagents in the users labgroup, and the number owned by the user.

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

Fetches the sorted reagent names associated with a labGroup.

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

Fetches concatinate of name and notes from Plasmids

fetchRenderingHints() - Static method in class gata.main.GATAUtil

Map of hints for high quality/ slow rendering

fetchRenderingHints() - Static method in class util.gen.Swing

Map of hints for high quality/ slow rendering

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

Returns a concatinate of the results where each String in the String[] represents a results table row where each column entry is separated by the divider String.

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

Returns a concatinate of the results where each String in the String[] represents a results table row where each column entry is separated by the divider String.

fetchSameNumberLines(BufferedReader, int) - Method in class trans.tpmap.MummerMapper

Loads the mummer results for one oligo into an ArrayList.

fetchSearchColumns() - Method in class bioroot.SearchBean

Extracts which columns to search for given group selections and field selections

fetchSeq(String) - Static method in class gata.plotter.ConservedSeqs

fetchSequence(String, int, int) - Method in class util.bio.seq.FetchIndexedSequence

Returns null if chromsome doesn't exist or the start or stop indexedSequence out of range.

fetchSequences() - Method in class gata.plotter.ConservedSeqs

fetchSequences(int[][]) - Method in class util.bio.seq.FetchIndexedSequence

Assumes startStop[index][0 start, 1 stop] is sorted by starts.

fetchSequences(String, int[][]) - Method in class util.bio.seq.FetchIndexedSequence

Returns null if chromsome doesn't exist or the start or stop indexedSequence out of range.

fetchSequences(String[]) - Static method in class util.bio.xamer.XamerCounter

Fetch all sequences from each multi-FASTA file

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

Returns a String[] of the items in a particular column.

fetchSingleColumn(String) - Method in class bioroot.DBUtil

Returns a int[] of the items in the first column.

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

Returns a String[] of the items in a particular column.

fetchStrainBeans(String, DBUtil) - Static method in class bioroot.strain.StrainSpreadSheet

Build StrainBean[] from Strain table in database.

fetchStrainTableRows(UserBean, StrainBean[], int[], DBUtil, boolean, boolean) - Static method in class bioroot.strain.StrainSpreadSheet

Returns table rows for every oligo according to a Preference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.

fetchSubSequence(int, int, int, String) - Static method in class util.bio.seq.Seq

Returns a sub sequence given a relative start and stop, the bp for the first base.

fetchSumaryLine() - Method in class util.bio.annotation.GeneGroup

fetchTabbedTableColumnRow(Feature[]) - Static method in class bioroot.Archive

Returns a table header row using the Preferece obj

fetchTableColumnRow(Preference, String) - Static method in class bioroot.Util

Returns a table header row using the Preferece obj and a reagentType: Oligo, Plasmid, Strain...

fetchTextCelFileIntensities(File) - Static method in class trans.misc.Util

Fetches intensity values from a text version cel file.

fetchTimedURLs(int, String[]) - Method in class util.amazon.S3Manager

Returns URLs to download particular objects from S3 that expire after a given amount of time.

fetchTopCenterY(Cluster) - Method in class util.bio.cluster.ClusterDrawPanel

Recurse through clusters always going higher to find center

fetchUserBean(HttpServletRequest, HttpServletResponse) - Static method in class bioroot.Util

Sets a guest user bean if there is none.

fetchUserName(int, boolean) - Method in class bioroot.DBUtil

Returns firstName lastName or lastName, firstName given a user id number

fetchValue(String) - Method in class trans.main.T2Parameter

fetchValueOptionGroup(String, String[]) - Static method in class util.gen.HTML

Returns a selected option group with the toSelect selected if present in the String[].

fileDescriptions - Variable in class cgar.CommitFiles

filepath - Static variable in class bioroot.Util

files - Variable in class cgar.CommitFiles

filter(Window[]) - Method in class trans.main.MergeWindowArrays

filter(int, Positive[]) - Static method in class trans.roc.Positive

Adds the bpOffSetEnds to the end of each Positive.

filterByStndDev() - Method in class trans.main.IntervalFilter

filterChromosomeSpecificFeatures(ArrayList, ArrayList) - Method in class trans.tpmap.TPMapProcessor

filterDNASeqLeaveWS(String) - Static method in class util.bio.seq.Seq

Deletes any non IUP characters but leaves whitespaces

filterDNASequence(String) - Static method in class util.bio.seq.Seq

Deletes any non IUP characters

filterDNASequenceStrict(String) - Static method in class util.bio.seq.Seq

Deletes any non GATCNX characters

filterField(String, int) - Static method in class util.gen.HTML

Filters a String for bad characters replacing them with html equivalents.

filterFields(String[], int) - Static method in class util.gen.HTML

Filters a String[] for bad characters replacing them with html equivalents.

filterGeneGroups(GeneGroup[], HashSet) - Static method in class trans.anno.AnnotateRegions

Returns an array of GeneGroup whose names were found in the Hash

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

Creates set number of intervals.

filterMapFeatures() - Method in class trans.tpmap.TPMapProcessor

filterRocWindows(RocWindow[], double, boolean) - Static method in class trans.roc.ParsePatternedWindows

Scans an array of RocWindow for those that are greater than (or less than if boolean is false) or equal to the cutOff.

filterSubWindow() - Method in class trans.main.IntervalFilter

Filters by the median ratio of the sub window

filterTPMap() - Method in class trans.tpmap.TPMapDuplicateFilter

filterWindowScore() - Method in class trans.main.IntervalFilter

filterWindows(Window[]) - Method in class trans.main.WindowBlockMakerTwoColor

Tosses any windows within the min max filter range.

findBestPair() - Method in class util.bio.cluster.HierarchicalClustering

Takes an ArrayList of VCluster and finds the best pair based on a PearsonCorrelationCoefficient.

findBiggestGenomicRegion(GenomicRegion[]) - Static method in class trans.graphics.GenomicRegion

Returns the length of the biggest GenomicRegion

findBin(Sgr) - Method in class trans.roc.MethodTester

Finds an appropriate bin given an sgr object

findBin(Sgr) - Method in class trans.roc.SgrBacCounter

Finds an appropriate bin given an sgr object

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

Given a value, finds the corresponding bin and returns the number of hits to that bin.

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

Returns the index of the containing bin or -1 if value is too small or big.

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

Attempts to join smallest chromosomes together so long as the combine file doesn't exceed the size of the biggest.

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

Finds the index of the key in the int[] but wont exceed the int[index]

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

Returns the index of the closest values[index] to the key.

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

Returns the index of the closest values[index] to the key.

findClosestPeak(BindingRegion[], BindingRegion[]) - Static method in class trans.anno.IntersectBindingPeaks

findClosestPeaks(Interval[], Interval[], File, File) - Method in class trans.main.OverlapCounter

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

Finds the index of the key in the int[] but wont preceed the int[index]

findDistToClosestATG(BindingRegion) - Method in class trans.anno.AnnotateRegions

Finds the distance to the closest ATG translation start site.

findDistToClosestATG(BindingRegion, ArrayList) - Method in class trans.anno.AnnotateRegions

findDistToClosestATG(BindingRegion) - Method in class trans.anno.AnnotateRegionsWithGeneList

Finds the distance to the closest ATG translation start site.

findDistToClosestATG(BindingRegion, ArrayList) - Method in class trans.anno.AnnotateRegionsWithGeneList

findDistToClosestTranscript(BindingRegion) - Method in class trans.anno.AnnotateRegions

Finds the distance to the closest ATG translation start site.

findDistToClosestTranscript(BindingRegion, ArrayList) - Method in class trans.anno.AnnotateRegions

findDistToClosestTranscript(BindingRegion, GeneGroup) - Method in class trans.anno.AnnotateRegions

Finds the distance to conservative estimate of start of first exon, returns 0 if overlaps.

findDistToClosestTranscript(BindingRegion) - Method in class trans.anno.AnnotateRegionsWithGeneList

Finds the distance to the closest ATG translation start site.

findDistToClosestTranscript(BindingRegion, ArrayList) - Method in class trans.anno.AnnotateRegionsWithGeneList

findDistToClosestTranscript(BindingRegion, GeneGroup) - Method in class trans.anno.AnnotateRegionsWithGeneList

Finds the distance to conservative estimate of start of first exon, returns 0 if overlaps.

findDistanceToATG(BindingRegion, GeneGroup) - Method in class trans.anno.AnnotateRegions

Finds the distance to conservative estimate of an ATG, returns 0 if overlaps.

findDistanceToATG(BindingRegion, GeneGroup) - Method in class trans.anno.AnnotateRegionsWithGeneList

Finds the distance to conservative estimate of an ATG, returns 0 if overlaps.

findEnds() - Method in class selex.SeqRead

findFlatTopPeak() - Method in class trans.main.PeakPicker

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

Finds and returns the biggest float in an float[].

findHighestInt(int[]) - Static method in class gata.main.GATAUtil

findHighestInt(int[]) - Static method in class util.gen.Num

Finds and returns the biggest int in an int[].

findHighestScore() - Method in class trans.main.PeakPicker

findHighestScoringWindow(int[][], double[], double[]) - Static method in class trans.main.FindSubBindingRegions

Returns a partially complete SubWindow.

findLowestScoringSeq(String[]) - Method in class meme.MotifScanner

Returns the lowest score from scoring all the seqs.

findMatch(IdNameMatch[], String) - Static method in class bioroot.IdNameMatch

findMaxIntIndex(int[]) - Static method in class util.gen.Num

Returns the first index containing the maximum value.

findMinMaxDoubleValues(double[]) - Static method in class util.gen.Num

Finds min and max values of a float array.

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

Finds min and max values of a float array.

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

Finds min and max values of an unsorted float array.

findMinMaxIntInt(int[][]) - Static method in class util.gen.Num

Finds min and max values of a int array.

findMinMaxIntValues(int[]) - Static method in class util.gen.Num

Finds min and max values of a int array.

findOligoMatches(UserBean, PlasmidBean[], DBUtil) - Static method in class bioroot.plasmid.PlasmidBase

Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user.

findOligos(UserBean, PlasmidBean, DBUtil) - Static method in class bioroot.plasmid.PlasmidBase

Uses Blast to find oligo matches to a plasmid from all the oligos in a labgroup visible to the user.

findOligos(UserBean, PlasmidBean[], DBUtil) - Static method in class bioroot.plasmid.PlasmidBase

Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user.

findPeak(Interval) - Static method in class trans.main.OverlapCounter

Returns base position of highest scoring peak, if no peak uses middle of sub window if no sub window uses middle of interval

findPeak() - Method in class trans.main.PeakPicker

findPeakBp(int) - Method in class trans.main.PeakPicker

findRandomRegion(int) - Method in class trans.anno.RandomRegions

Attempt to find a random Region of the appropriate minimum length.

findRandomSegment(Region, int) - Method in class trans.anno.RandomRegions

Returns a random segment of the appropriate length within the region.

findRegion(GenomicRegion[], Point2D) - Method in class trans.graphics.RankedSetDrawPanel

Scans an array of GenomicRegions Rectangles to see if the Point is present, ie they clicked it.

findSequenceHits(String[], String) - Static method in class util.bio.xamer.XamerCounter

Looks for an exact match of the oligo to each of the seqs, returning the seqs that contain the oligo

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

Finds the start and stop indexes given a sorted int[] of values and two values, one after the other, close together, otherwise just use Arrays.binarySearch.

findStartStopThresholds(double, double) - Method in class trans.roc.RocWindowScanner

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

Creates set number of intervals.

findTargetFDRThreshold(double, int) - Method in class trans.roc.RocWindowScanner

Attempts to find a threshold that gives the target FDR, will run through maxCycles and return closest threshold if targetFDR is not reached.

findWindow(Window[]) - Method in class trans.main.MultiWindowIntervalMaker

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

Scans a float array for zeros, if found returns true, other wise returns false.

fireMeme(String) - Method in class meme.MemeParser

fireMeme() - Method in class meme.MemeR

fireMemeParallel(String, String, String, String) - Method in class meme.MemeParser

Fires meme using a shell script and qsub, checks every 15 sec to see if done, returns unparsed MEME output.

fireQSub(String, String, String, boolean) - Static method in class util.gen.IO

Fires qsub with the commands, will wait and return results and delete x.sh and the output files if you like.

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

Fires qsub with the commands.

floatArrayToString(float[], String) - Static method in class util.gen.Misc

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

flushBase64() - Method in class com.amazon.thirdparty.Base64.OutputStream

Method added by PHIL.

focusGained(FocusEvent) - Method in class gata.aligner.FileFocusListener

focusLost(FocusEvent) - Method in class gata.aligner.FileFocusListener

formatNumber(double, int) - Static method in class util.gen.Num

Converts a double ddd.dddddddd to a user determined number of decimal places right of the .

formatNumberOneFraction(double) - Static method in class util.bio.calc.NucleicAcid

Takes a double returns a String with one fractional digit 9.54443 -> 9.5

formatNumberOneFraction(double) - Static method in class util.gen.Num

Converts a double ddd.dddddddd to sss.s

formatPercentOneFraction(double) - Static method in class util.bio.calc.NucleicAcid

Takes a double in percent returns a String with one fraction 0.85842 -> 85.8%

formatPercentOneFraction(double) - Static method in class util.gen.Num

Converts 0.345543 to 34.6%

formattedInfo(GenomicRegion) - Method in class trans.graphics.RankedSetDrawPanel

fractionPositive(ArrayList, double, double) - Static method in class trans.roc.MethodTester

Given an ArrayList of Double, calculates the fraction that is >= scoreCutOff.

fractionPositive(ArrayList, double, double) - Static method in class trans.roc.SgrBacCounter

Given an ArrayList of Double, calculates the fraction that is >= scoreCutOff.

fractionTotalIntersection(GenomicRegion[]) - Method in class trans.graphics.RankedSetAnalysis

Returns the total fraction of intersection.

fullPathToBlast - Static variable in class bioroot.Util