Index

A B C D E F G H I J L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

F

factorial(int) - Static method in class bacnet.utils.MathUtils

Calculate the factorial of n

FASTA - Enum constant in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat

FastaFileReader<S extends Sequence<?>,C extends Compound> - Class in bacnet.reader

FastaFileReader(File, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class bacnet.reader.FastaFileReader

If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.

FastaFileReader(InputStream, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class bacnet.reader.FastaFileReader

If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

FastaGeneWriter - Class in org.biojava3.core.sequence.io

A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.

FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean) - Constructor for class org.biojava3.core.sequence.io.FastaGeneWriter

FastaGeneWriter(OutputStream, Collection<GeneSequence>, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound>, boolean, int) - Constructor for class org.biojava3.core.sequence.io.FastaGeneWriter

FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava3.core.sequence.io.template

FastaHeaderParserInterface<S extends Sequence<?>,C extends Compound> - Interface in org.biojava3.core.sequence.io.template

FastaReader<S extends Sequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io

Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files

FastaReader(File, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava3.core.sequence.io.FastaReader

If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.

FastaReader(InputStream, FastaHeaderParserInterface<S, C>, SequenceCreatorInterface<C>) - Constructor for class org.biojava3.core.sequence.io.FastaReader

If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

FastaReaderHelper - Class in org.biojava3.core.sequence.io

FastaReaderHelper() - Constructor for class org.biojava3.core.sequence.io.FastaReaderHelper

FastaSequenceParser - Class in org.biojava3.core.sequence.io

Used to parse a stream of a fasta file to get the sequence

FastaSequenceParser() - Constructor for class org.biojava3.core.sequence.io.FastaSequenceParser

FastaWriter<S extends Sequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io

The FastaWriter writes a collection of sequences to an outputStream.

FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>) - Constructor for class org.biojava3.core.sequence.io.FastaWriter

Use default line length of 60

FastaWriter(OutputStream, Collection<S>, FastaHeaderFormatInterface<S, C>, int) - Constructor for class org.biojava3.core.sequence.io.FastaWriter

Set custom lineLength

FastaWriterHelper - Class in org.biojava3.core.sequence.io

The class that should be used to write out fasta file of a sequence collection

FastaWriterHelper() - Constructor for class org.biojava3.core.sequence.io.FastaWriterHelper

FC - Enum constant in enum bacnet.datamodel.dataset.OmicsData.ColNames

FC - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat

FC - Enum constant in enum bacnet.table.core.ColorMapper.TypeMapper

FC - Enum constant in enum bacnet.table.core.ColorMapperRCP.Type

FDR - Class in bacnet.scripts.core.stat

FDR() - Constructor for class bacnet.scripts.core.stat.FDR

FDRBH - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat

FDRBONF - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat

FDRBY - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat

Feature - Class in org.biojava3.genome.parsers.gff

A Feature corresponds to a single row in a GFF file.

Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava3.genome.parsers.gff.Feature

Construct a new Feature from raw data (usually a GFF row).

Feature(Feature) - Constructor for class org.biojava3.genome.parsers.gff.Feature

Make a copy of the specified feature.

FeatureHelper - Class in org.biojava3.genome.parsers.gff

FeatureHelper() - Constructor for class org.biojava3.genome.parsers.gff.FeatureHelper

FeatureI - Interface in org.biojava3.genome.parsers.gff

A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.

FeatureInterface<S extends AbstractSequence<C>,C extends Compound> - Interface in org.biojava3.core.sequence.features

Interface class to handle describing arbitrary features.

FeatureList - Class in org.biojava3.genome.parsers.gff

A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.

FeatureList() - Constructor for class org.biojava3.genome.parsers.gff.FeatureList

Construct an empty list.

FeatureList(Collection<FeatureI>) - Constructor for class org.biojava3.genome.parsers.gff.FeatureList

Construct a new list containing the same features as the specified list.

FeaturesKeyWordInterface - Interface in org.biojava3.core.sequence.features

Models the keywords that are annotated for a protein sequence at Uniprot.

Febit - Class in bacnet.scripts.listeriomics.technology

Febit() - Constructor for class bacnet.scripts.listeriomics.technology.Febit

FILE_SEPARATOR - Static variable in class bacnet.scripts.database.HomologCreation

We added manually this variable because when running .bat file on windows the file separator can get tricky.

FileAccessError - Error in org.biojava3.core.exceptions

Thrown from SequenceFileProxyLoader if error opening file using RandomnAccessFile

FileAccessError(String) - Constructor for error org.biojava3.core.exceptions.FileAccessError

fileExtension(BlastOutput.BlastOutputTYPE) - Static method in class bacnet.scripts.blast.BlastOutput

For a specific type, return the extension of the corresponding file

fileExtension(BlastOutput.BlastOutputTYPE) - Static method in class bacnet.scripts.database.HomologCreation

For a specific type, return the extension of the corresponding file

FileProxyDNASequenceCreator - Class in org.biojava3.core.sequence.io

This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.

FileProxyDNASequenceCreator(File, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator

Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

FileProxyProteinSequenceCreator - Class in org.biojava3.core.sequence.io

This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.

FileProxyProteinSequenceCreator(File, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator

Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

FileUtils - Class in bacnet.utils

Utils for file manipulation.

FileUtils() - Constructor for class bacnet.utils.FileUtils

filter(ExpressionMatrix, Filter) - Static method in class bacnet.utils.ExpressionMatrixStat

Apply a filter to an ExpressionMatrix

Filter - Class in bacnet.table.core

Filter - Class in bacnet.utils

Filter() - Constructor for class bacnet.table.core.Filter

Filter() - Constructor for class bacnet.utils.Filter

Filter(ExpressionMatrix) - Constructor for class bacnet.table.core.Filter

Filter(ExpressionMatrix) - Constructor for class bacnet.utils.Filter

Filter.TypeFilter - Enum in bacnet.table.core

Filter.TypeFilter - Enum in bacnet.utils

filterAM(ExpressionMatrix) - Static method in class bacnet.scripts.core.stat.LPE

Delete values inferior to 0 in am matrix which as been sorted by A values

filterCopyResults(String, String) - Static method in class bacnet.scripts.genome.SDProfile

Filters all files by deleting all positive results, and inverting energies.

filterData(ArrayList<String>) - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView

We filter data, and add all comparisons from the data

FilterDialog - Class in bacnet.table.gui

Dialog for managing Filter for ExpressionMatrix

FilterDialog(Filter, Shell) - Constructor for class bacnet.table.gui.FilterDialog

Create the dialog.

filterDiffSize(ArrayList<BlastResult>, int) - Static method in class bacnet.scripts.blast.BlastResult

filterEGDe(ExpressionMatrix) - Static method in class bacnet.scripts.listeriomics.technology.GeneralArray

Keep only the row containing EGD-e genes: "lmo" gene

filterEGDe(ExpressionMatrix) - Static method in class bacnet.scripts.listeriomics.technology.JCVI

Keep only the row containing EGD-e genes: "lmo" gene

filterEGDe(ExpressionMatrix) - Static method in class bacnet.scripts.listeriomics.technology.WUSTL

Keep only the row containing EGD-e genes: "lmo" gene

FilterExpressionMatrixDialog - Class in bacnet.table.gui

Dialog displaying the list of Filters currently used on the ExpressionMatrix

FilterExpressionMatrixDialog(FilterList, Shell) - Constructor for class bacnet.table.gui.FilterExpressionMatrixDialog

Create the dialog.

filterF2365(ExpressionMatrix) - Static method in class bacnet.scripts.listeriomics.technology.GeneralArray

Keep only the row containing F2365 genes: "LMOf2365" gene

filterF2365(ExpressionMatrix) - Static method in class bacnet.scripts.listeriomics.technology.JCVI

Keep only the row containing F2365 genes: "LMOf2365" gene

filterF2365(ExpressionMatrix) - Static method in class bacnet.scripts.listeriomics.technology.WUSTL

Keep only the row containing F2365 genes: "LMOf2365" gene

filterHCC23(ExpressionMatrix) - Static method in class bacnet.scripts.listeriomics.technology.JCVI

Keep only the row containing HCC23 genes: "LMHCC" gene

filterIdentities(ArrayList<BlastResult>, int) - Static method in class bacnet.scripts.blast.BlastResult

Use identities to filter a list of BlastResult

filterLength(ArrayList<BlastResult>, int) - Static method in class bacnet.scripts.blast.BlastResult

FilterList - Class in bacnet.table.core

FilterList() - Constructor for class bacnet.table.core.FilterList

FilterList(ExpressionMatrix) - Constructor for class bacnet.table.core.FilterList

filterNetwork() - Method in class bacnet.views.CoExprNetworkView

Using genome elements selected and current cut-off.

filterNetwork(ArrayList<String>, double) - Method in class bacnet.datamodel.dataset.Network

Given a list of vertice and a cutoff, filter the network

filterSmallORF(ArrayList<String>, double) - Static method in class bacnet.scripts.blast.MultiSequenceBlastProtein

Filtering table of results by e-value

filterSmallORF(ArrayList<String>, double) - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein

Filtering table of results by e-value

filterValue(double) - Method in class bacnet.table.core.Filter

filterValue(double) - Method in class bacnet.utils.Filter

findCodonUsage(String) - Static method in class bacnet.datamodel.proteomics.NTermCreateData

Get Codon usage of the peptide

findColumn(String[][], String) - Static method in class bacnet.utils.ArrayUtils

Find the index of a column, given its header

findEGDePosition() - Static method in class bacnet.scripts.listeriomics.srna.Srna10403SOliver

Get all Srna from Oliver et al. 2009 list, get Sequence in 10403S pseudo_chromosome
Run BlastN on EGD-e.
When Blast are all performed, summarize information in a Table.
Choose which rli to keep

findLeaderLess() - Static method in class bacnet.scripts.listeriomics.nterm.NTermMain

Search for upstream TSS for each NTerm
It uses list of aTIS

findLocusTag(String) - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics

findLocusTag(String, String) - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics

Search a locustag in all GFF present for a genomeName

findMissingCELfilesListeria() - Static method in class bacnet.scripts.database.BioConditionCreation

Read Array in expDesignTableFile and search which Raw data is missing
Save missing .CEL and .txt files in three lists: NotFoundCEl GeneExpr.txt NotFoundCEl Tiling.txt NotFoundCEl RNASeq.txt

findModifs() - Method in class bacnet.datamodel.proteomics.TIS

List the type of modification overlap of each NTerm

findNextNterm(int, String) - Method in class bacnet.datamodel.dataset.NTermData

Given a position in the genome, give the NTerm just downstream to it

findNTermRef() - Method in class bacnet.datamodel.proteomics.TIS

Find the Nterm with the highest spectrum

findORFSequence(String, String) - Static method in class bacnet.scripts.blast.MultiSequenceBlastProtein

Go through fasta file and extract sequence

findOverlaps() - Method in class bacnet.datamodel.proteomics.TIS

List the type of gene overlap of each NTerm

findPosition() - Method in class bacnet.datamodel.proteomics.TIS

From all the nTerms (supposed in the same strand), get the minimal begin and the maximum end

findPreviousNterm(int, String) - Method in class bacnet.datamodel.dataset.NTermData

Given a position in the genome, give the NTerm just upstream to it

findProbes() - Static method in class bacnet.scripts.arrayexpress.ArrayExpressTechnology

From array probe sequence try to retrieve the gene name

findProbes() - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology

From array probe sequence try to retrieve the gene name

findRefSequence() - Method in class bacnet.datamodel.proteomics.TIS

Find the total sequence of all peptides

findSameNterm(int, String) - Method in class bacnet.datamodel.dataset.NTermData

Given a position in the genome, give the NTerm just upstream to it

findSDSequence(String) - Static method in class bacnet.datamodel.proteomics.NTermCreateData

For each NTerm calculates anti Shine-Dalgarno sequence affinity in the region -20bp before peptide on the genome

findSDSequenceforLMO() - Static method in class bacnet.datamodel.proteomics.NTermUtils

Find SD binding free energy on region -20bp upstream to each lmo

findSmallORFSequence(String, String) - Static method in class bacnet.scripts.blast.MultiSequenceBlastProtein

Go through fasta file and extract sequence

findStart(String) - Static method in class bacnet.datamodel.proteomics.NTermCreateData

Search if the first amino acid or the amino acid before is a StartCodon

findTSS(String) - Static method in class bacnet.datamodel.proteomics.NTermCreateData

Deprecated.

FLAT - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE

FLAT_SHOW - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE

FlatFileCache - Class in org.biojava3.core.util

Provides a cache for storing multiple small files in memory.

foldChange(double[], double[]) - Static method in class bacnet.scripts.core.stat.StatUtils

foldChange(double, double) - Static method in class bacnet.scripts.core.stat.StatUtils

Calculate ratio value1/value2

foldChangeGeneExpression(double[], double[], boolean) - Static method in class bacnet.scripts.core.stat.StatUtils

Vector1 and Vectior2 correspond to three technical replicates, so:
We calculate the fold change by measuring the relative expression (or ratio) of the median expression of vector1 and vector2

foldChangeGeneExpressionWT(double[], double, boolean) - Static method in class bacnet.scripts.core.stat.StatUtils

Use this fonction when comparing a vector to a median value already calculated
For example when vector2Median is equal to WT average expression

foldChangeTiling(double[], double[], boolean) - Static method in class bacnet.scripts.core.stat.StatUtils

Vector1 and vector2 are the values of all the probes contained in a specific genome element, so:
We calculate the difference within vector1-vector2 (probe by probe) And then calculate the median the resulting vector

foldChangeTilingWT(double[], double, boolean) - Static method in class bacnet.scripts.core.stat.StatUtils

folderCreation(String) - Static method in class bacnet.scripts.database.HomologCreation

foldRNA(Sequence, String, boolean) - Static method in class bacnet.scripts.core.UNAfold

For a specific sequence, get its RNA sequence and fold it
Calculate possible free energies
transform results into annotation file
Display using sir_graph

foldRNA(Sequence, String, boolean) - Static method in class bacnet.utils.UNAfold

For a specific sequence, get its RNA sequence and fold it
Calculate possible free energies
transform results into annotation file
Display using sir_graph

foldRNA(String, String, String, boolean) - Static method in class bacnet.scripts.core.UNAfold

For a specific sequence, get its RNA sequence and fold it
Calculate possible free energies
transform results into annotation file
Display using sir_graph

foldRNA(String, String, String, boolean) - Static method in class bacnet.utils.UNAfold

For a specific sequence, get its RNA sequence and fold it
Calculate possible free energies
transform results into annotation file
Display using sir_graph

For - Enum constant in enum bacnet.datamodel.proteomics.NTerm.TypeModif

formatSequence(Genome) - Static method in class bacnet.reader.GBKReader

foundSDSequence() - Method in class bacnet.datamodel.sequence.Sequence

Search the consensus SD sequence in the 20bp upstream to a Sequence

FourBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

FourBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

FourBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

FourBitArrayWorker(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker

FourBitSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage

Four bit encoding of the bit formats.

FourBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(FourBitSequenceReader.FourBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.FourBitSequenceReader

FourBitSequenceReader.FourBitArrayWorker<C extends Compound> - Class in org.biojava3.core.sequence.storage

A four bit per compound implementation of the bit array worker code.

frame() - Method in class org.biojava3.genome.parsers.gff.Feature

Get frame (aka phase).

Frame - Enum in org.biojava3.core.sequence.transcription

Indicates a way of translating a sequence.

fromArraytoList(String[][]) - Static method in class bacnet.utils.ArrayUtils

Transform an array into a List of rows

fromBio(int, int, char) - Static method in class org.biojava3.genome.parsers.gff.Location

Create location from "biocoordinates", as in GFF file.

fromBioExt(int, int, char, int) - Static method in class org.biojava3.genome.parsers.gff.Location

Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.

FTP_Path - Static variable in class bacnet.scripts.arrayexpress.ArrayExpressDataImport

FTP_URL - Static variable in class bacnet.scripts.arrayexpress.ArrayExpressTechnology

FTP_URL - Static variable in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology

FULL_SEQUENCE_DATA - Enum constant in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage

fusion(String[][], String[][], boolean) - Static method in class bacnet.utils.ArrayUtils

Return a new Array of String which is the fusion of both array If header = true; the first row of array2 is conserved

fusionProteinUTRDB() - Static method in class bacnet.scripts.blast.ProteinTools

Fusion ProteinDB and UTRDB in one file

fusionProteinUTRDB() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase

Fusion ProteinDB and UTRDB in one file

FuzzyPoint - Class in org.biojava3.core.sequence.location

Implementation for resolving fuzzy locations.

FuzzyPoint(int, int) - Constructor for class org.biojava3.core.sequence.location.FuzzyPoint

FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>) - Constructor for class org.biojava3.core.sequence.location.FuzzyPoint

FuzzyPoint(int, int, Point.Resolver<FuzzyPoint>, boolean, boolean) - Constructor for class org.biojava3.core.sequence.location.FuzzyPoint

A B C D E F G H I J L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form