E-Index

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E

ECOLI_NAME - Static variable in class bacnet.datamodel.sequence.Genome: Name for Ecoli genome
edit(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
edit(Sequence<C>) - Method in interface org.biojava3.core.sequence.edits.Edit
Edit<C extends Compound> - Interface in org.biojava3.core.sequence.edits: Interface for carrying out edit operations on a Sequence.
Edit.AbstractEdit<C extends Compound> - Class in org.biojava3.core.sequence.edits: Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together with a target Sequence.
Edit.Delete<C extends Compound> - Class in org.biojava3.core.sequence.edits: Implementation which allows for the deletion of bases from a Sequence
Edit.Insert<C extends Compound> - Class in org.biojava3.core.sequence.edits: Edit implementation which allows us to insert a base at any position in a Sequence.
Edit.Substitute<C extends Compound> - Class in org.biojava3.core.sequence.edits: Allows for the substitution of bases into an existing Sequence.
EGDC_NAME - Static variable in class bacnet.datamodel.sequence.Genome: Name of EGD genome
EGDE_ANNOTATION - Static variable in class bacnet.datamodel.annotation.Annotation: All supplementary information taken from Glaser et al., Science 2001
EGDE_CHROMO_NAME - Static variable in class bacnet.datamodel.sequence.Genome: Name of EGD-e chromosomegenome
EGDE_NAME - Static variable in class bacnet.datamodel.sequence.Genome: Name of EGD-e genome
EGDE_RAST_NAME - Static variable in class bacnet.datamodel.sequence.Genome: Name of RAST EGD-e genome
EGDE_SUPPTABLE - Static variable in class bacnet.datamodel.annotation.Annotation: All supplementary information taken from Toledo-Arana et al., Nature 2009
EGDeWTdata - Class in bacnet.datamodel.dataset: List of method for creating EGDe_Mean data: A data created from the mean of all Wild Type data (37C in BHI)
EGDeWTdata() - Constructor for class bacnet.datamodel.dataset.EGDeWTdata
eliminateColumn(double[][]) - Static method in class bacnet.utils.ArrayUtils
EM - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
EMPTY - Static variable in interface org.biojava3.core.sequence.location.template.Location: Basic location which is set to the minimum and maximum bounds of Integer.
ENA - Enum constant in enum org.biojava3.core.sequence.DataSource
encodeToFile(Object, String) - Static method in class bacnet.utils.XMLUtils: Serialisation d'un objet dans un fichier
end - Variable in class bacnet.scripts.blast.BlastResult
end() - Method in class org.biojava3.genome.parsers.gff.Location: Get the ending index.
endQuery - Variable in class bacnet.scripts.blast.BlastResult
endsAfter(Location) - Method in class org.biojava3.genome.parsers.gff.Location: Check if this location ends after other location ends.
endsBefore(Location) - Method in class org.biojava3.genome.parsers.gff.Location: Check if this location ends before other location ends.
entrySet() - Method in class org.biojava3.core.util.SoftHashMap
equal(boolean, boolean) - Static method in class org.biojava3.core.util.Equals
equal(int, int) - Static method in class org.biojava3.core.util.Equals
equal(long, long) - Static method in class org.biojava3.core.util.Equals
equal(Object, Object) - Static method in class org.biojava3.core.util.Equals
equals(Object) - Method in class bacnet.datamodel.proteomics.NTerm
equals(Object) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Override of equals method from Object To be equal two genome has to come from the same species.
equals(Object) - Method in class org.biojava3.core.sequence.AccessionID
equals(Object) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompound
equals(Object) - Method in class org.biojava3.core.sequence.compound.CodonCompound
equals(Object) - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
equals(Object) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
equals(Object) - Method in class org.biojava3.core.sequence.location.SimplePoint
equals(Object) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
equals(Object) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
equals(Object) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
equals(Object) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
equals(Object) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
equals(Object) - Method in class org.biojava3.core.sequence.template.AbstractCompound
equals(Object) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
equals(Object) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
equals(Object) - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
equals(Object) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
equals(Location) - Method in class org.biojava3.genome.parsers.gff.Location: Compare locations for equality.
Equals - Class in org.biojava3.core.util: A set of helper methods which return true if the two parameters are equal to each other.
Equals() - Constructor for class org.biojava3.core.util.Equals
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompound
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.compound.CodonCompound
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.template.AbstractCompound
equalsIgnoreCase(Compound) - Method in interface org.biojava3.core.sequence.template.Compound
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
equalsIgnoreCase(Compound) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
equalsToIgnoreEndline(String, String) - Static method in class org.biojava3.core.util.StringManipulationHelper: compares two strings for equality, line by line, ignoring any difference of end line delimiters contained within the 2 Strings.
equalsToXml(String, String) - Static method in class org.biojava3.core.util.StringManipulationHelper
equivalent(String, boolean) - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Given a sequence name, it gives the conservation in the three different species, in a String[]:
estimate(ExpressionMatrix) - Static method in class bacnet.scripts.core.stat.LPE
euclideanDistance(double[][]) - Static method in class bacnet.utils.ArrayUtils: Calcul of euclidean distance Matrix
euclideanDistance(double[], double[]) - Static method in class bacnet.utils.VectorUtils: Calculate euclidean distance between vector x and vector y
eValue - Variable in class bacnet.scripts.blast.BlastResult
execute(IWorkbench, Shell) - Method in class bacnet.handler.LoadExpressionMatrixHandler
exists(String) - Static method in class bacnet.utils.FileUtils: Test if a file exists or not
ExonComparator - Class in org.biojava3.core.sequence: Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.
ExonComparator() - Constructor for class org.biojava3.core.sequence.ExonComparator
ExonSequence - Class in org.biojava3.core.sequence: A gene contains a collection of Exon sequences
ExonSequence(GeneSequence, int, int) - Constructor for class org.biojava3.core.sequence.ExonSequence: Need a parent gene sequence and the bioBegin and bioEnd.
Experiment - Class in bacnet.datamodel.expdesign
Experiment() - Constructor for class bacnet.datamodel.expdesign.Experiment
Experiment(String) - Constructor for class bacnet.datamodel.expdesign.Experiment
exportInHTML(JTable, String) - Static method in class bacnet.utils.TableHTMLExport
Expression - Class in bacnet.scripts.core: A list of methods to combine transcriptomics data in ExpressionMatrix
Expression(Genome, ArrayList<String>, ArrayList<BioCondition>, OmicsData.TypeData) - Constructor for class bacnet.scripts.core.Expression: Create Expression object to regroups multiple Expression data
ExpressionData - Class in bacnet.datamodel.dataset: Abstract Class describing data related to transcriptome
This data are saved in DataStream and might be read in streaming mode

boolean[] read is used as a "read" indicator
As soon as a position in double[] values has been read, boolean[] read is updated
ExpressionData() - Constructor for class bacnet.datamodel.dataset.ExpressionData
ExpressionData(String) - Constructor for class bacnet.datamodel.dataset.ExpressionData
ExpressionMatrix - Class in bacnet.datamodel.dataset: This is the principal data model used in the software for managing big table of expression
ExpressionMatrix - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
ExpressionMatrix() - Constructor for class bacnet.datamodel.dataset.ExpressionMatrix
ExpressionMatrix(String, int) - Constructor for class bacnet.datamodel.dataset.ExpressionMatrix
ExpressionMatrix(ArrayList<String>) - Constructor for class bacnet.datamodel.dataset.ExpressionMatrix: Create a void ExpressionMatrix and associate headers
ExpressionMatrixReader - Class in bacnet.reader
ExpressionMatrixReader() - Constructor for class bacnet.reader.ExpressionMatrixReader
ExpressionMatrixStat - Class in bacnet.utils: List of method for doing Stat on ExpressionMatrices
ExpressionMatrixStat() - Constructor for class bacnet.utils.ExpressionMatrixStat
EXTENSION - Static variable in class bacnet.datamodel.annotation.Signature
EXTENSION - Static variable in class bacnet.datamodel.dataset.GeneExpression
EXTENSION - Static variable in class bacnet.datamodel.dataset.NGS
EXTENSION - Static variable in class bacnet.datamodel.dataset.OmicsData: Extension name of every OmicsData serialized
EXTENSION - Static variable in class bacnet.datamodel.dataset.Tiling
EXTENSION - Static variable in class bacnet.genomeBrowser.core.Track
EXTENSION - Static variable in class bacnet.reader.GFFNCBIReader
EXTENSION - Static variable in class bacnet.reader.PTTReader
extractAllContigs(boolean) - Static method in class bacnet.scripts.blast.GenomeNCBIFolderTools: Go through all folders of Genome directory and extract all TGZ contained in .faa .fna .ffn .frn .gff
extractAllSrnaToGff() - Static method in class bacnet.datamodel.sequence.Srna: Extract to a GFF file the list of Srna from EGD-e
extractGZIP(String, String) - Static method in class bacnet.utils.FileUtils
extractInfo(ArrayList<Srna>) - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: From Blast Result extract Genome containing the sRNA
A filter is applied to keep results with identities above 50%
extractInfo(ArrayList<String>, String, String, double, boolean) - Static method in class bacnet.scripts.blast.Blast: From Blast Result extract Genome containing the sRNA
extractInformation(BioCondition) - Static method in class bacnet.scripts.core.normalization.GENormalization: Load .ge files resulting from R script normalization and extract the important columns = column 0-4 = log Expression values and median expression
extractInformation(Experiment) - Static method in class bacnet.scripts.core.normalization.GENormalization: Extract information contained in all .ge files of the experiment
extractList(ArrayList<String>, int, int) - Static method in class bacnet.scripts.database.HomologCreation: Extract a portion of an ArrayList into another ArrayList
extractPhylogeny(Phylogeny, HashMap<String, String[]>) - Static method in class bacnet.scripts.phylogeny.PhylogenyTools: If a node of the Phylogeny phy, is not a key of infoNodes Map, delete the tree
return the subTree obtained
extractPhylogeny(Phylogeny, TreeSet<Integer>) - Static method in class bacnet.scripts.phylogeny.PhylogenyToolsJolley: If a node of the Phylogeny phy, is include in listIDs, delete the node
extractPosition(Srna, Genome, TreeMap<String, String>) - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: From Blast Result extract position in the Genome of each sRNA
Srna with an identity lower than 25% are not inserted
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Febit
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.GeneralArray
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.IHM
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.JCVI
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.LT
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Macroarray
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.NimbleGen
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Tasmania
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.UGiessen
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Wuerzburg
extractProbes(String, String) - Static method in class bacnet.scripts.listeriomics.technology.WUSTL
extractProbes(String, String, String) - Static method in class bacnet.scripts.listeriomics.technology.Agilent
extractProbesComparison(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Agilent: Extract Probes from Matrix when its a Comparison
extractProbesComparison(String, String, boolean) - Static method in class bacnet.scripts.listeriomics.technology.CUFSL: Extract Probes from Matrix when its a Comparison

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