G-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

G

gaps - Variable in class bacnet.scripts.blast.BlastResult
GBKReader - Class in bacnet.reader: GenBankl reader tools
TO BE FIXED for adding other chromosomes
GBKReader() - Constructor for class bacnet.reader.GBKReader
GCG - Enum constant in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat
GCStats - Class in org.biojava3.genome.parsers.gff
GCStats() - Constructor for class org.biojava3.genome.parsers.gff.GCStats
GElement - Class in bacnet.genomeBrowser.tracksGUI: Here are all the methods for displaying each Genome element
GElement() - Constructor for class bacnet.genomeBrowser.tracksGUI.GElement
GENBANK - Enum constant in enum org.biojava3.core.sequence.DataSource
Gene - Class in bacnet.datamodel.sequence
Gene - Enum constant in enum bacnet.datamodel.sequence.Sequence.SeqType
Gene() - Constructor for class bacnet.datamodel.sequence.Gene
Gene(String, int, int, char) - Constructor for class bacnet.datamodel.sequence.Gene
GENE - Static variable in class bacnet.raprcp.NavigationManagement
GeneExpr - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
GeneExpression - Class in bacnet.datamodel.dataset: GeneExpression array data from Listeria tiling chip ArrayExpress id : A-AFFY-140 Here double[] values vector has length = 5*probes.size because we put 5 columns column 0-2 = 3 replicatas column 3 = median expression column 4 = var expression
GeneExpression() - Constructor for class bacnet.datamodel.dataset.GeneExpression
GeneExpression(String) - Constructor for class bacnet.datamodel.dataset.GeneExpression
GeneFeatureHelper - Class in org.biojava3.genome: Allow to process genome elements annotation
GeneFeatureHelper() - Constructor for class org.biojava3.genome.GeneFeatureHelper
GeneIDGFF2Reader - Class in org.biojava3.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneIDGFF2Reader() - Constructor for class org.biojava3.genome.parsers.gff.GeneIDGFF2Reader
GeneIDXMLReader - Class in org.biojava3.genome.parsers.geneid
GeneIDXMLReader(String) - Constructor for class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
GeneMarkGTFReader - Class in org.biojava3.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneMarkGTFReader() - Constructor for class org.biojava3.genome.parsers.gff.GeneMarkGTFReader
GeneNCBITools - Class in bacnet.datamodel.sequenceNCBI: List of tools useful to extract information hidden in the NoteList of a DNASequence
GeneNCBITools() - Constructor for class bacnet.datamodel.sequenceNCBI.GeneNCBITools
GENERAL - Enum constant in enum org.biojava3.core.sequence.DataSource
GENERAL_WT_DATA - Static variable in class bacnet.datamodel.dataset.OmicsData: Name of the Transcriptome data used as a reference data for comparisons
GENERAL_WT_NAME - Static variable in class bacnet.datamodel.dataset.OmicsData: Name used for "median" data created from a set of reference condition
GeneralArray - Class in bacnet.scripts.listeriomics.technology
GeneralArray() - Constructor for class bacnet.scripts.listeriomics.technology.GeneralArray
GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> - Class in org.biojava3.core.sequence.io: We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.
GenericFastaHeaderFormat() - Constructor for class org.biojava3.core.sequence.io.GenericFastaHeaderFormat
GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.io: The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterface GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE PDB EBI PDB:1ECY_A mol:protein length:142 ECOTIN Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
GenericFastaHeaderParser() - Constructor for class org.biojava3.core.sequence.io.GenericFastaHeaderParser
GeneSequence - Class in org.biojava3.core.sequence
GeneSequence(ChromosomeSequence, int, int, Strand) - Constructor for class org.biojava3.core.sequence.GeneSequence: A class that keeps track of the details of a GeneSequence which is difficult to properly model.
GeneView - Class in bacnet.sequenceTools
GeneView() - Constructor for class bacnet.sequenceTools.GeneView
GeneViewHomologTools - Class in bacnet.sequenceTools: All the tools to display homologs in the Gene Panel view: - It creates the homolog table - Create the homolog figure - Display both of them
GeneViewHomologTools() - Constructor for class bacnet.sequenceTools.GeneViewHomologTools
GeneViewLocalizationTools - Class in bacnet.sequenceTools
GeneViewLocalizationTools() - Constructor for class bacnet.sequenceTools.GeneViewLocalizationTools
GeneViewProteomeTools - Class in bacnet.sequenceTools
GeneViewProteomeTools() - Constructor for class bacnet.sequenceTools.GeneViewProteomeTools
GeneViewTranscriptomeTools - Class in bacnet.sequenceTools
GeneViewTranscriptomeTools() - Constructor for class bacnet.sequenceTools.GeneViewTranscriptomeTools
GENINFO - Enum constant in enum org.biojava3.core.sequence.DataSource
genome - Variable in class bacnet.scripts.genome.CircularGenomeJPanel
Genome - Class in bacnet.datamodel.sequence: Class for managing Genome
Contains all Genes, non-coding RNA and all other elements found in the genome GFF GFFNCBIReader
Genome() - Constructor for class bacnet.datamodel.sequence.Genome
Genome(String, boolean) - Constructor for class bacnet.datamodel.sequence.Genome: Create a Genome from .fna, .annot, and all serialized Sequence object:
Read Genome sequence information in the different fna files
Load annotation information

As we are dealing with bacteria, we are sure that the chromosome with maximum length is THE chromosome, other are plasmids.
GENOME - Static variable in class bacnet.raprcp.NavigationManagement
GENOME_PATH - Static variable in class bacnet.scripts.listeriomics.srna.SmallPeptidesSearch: Deprecated.
Genome.GetMultiFastaThread - Class in bacnet.datamodel.sequence
Genome.OpenGenomesThread - Class in bacnet.datamodel.sequence
GenomeConversion - Class in bacnet.datamodel.sequenceNCBI: Static methods for converting GenomeNCBI to Genome
Genome is used for fast loading of all genomic information we gathered
GenomeConversion() - Constructor for class bacnet.datamodel.sequenceNCBI.GenomeConversion
GenomeConversionElement - Class in bacnet.datamodel.sequenceNCBI
GenomeConversionElement() - Constructor for class bacnet.datamodel.sequenceNCBI.GenomeConversionElement
GenomeElementAtlas - Class in bacnet.expressionAtlas.core
GenomeElementAtlas() - Constructor for class bacnet.expressionAtlas.core.GenomeElementAtlas
GenomeElementAtlas(Sequence, Filter, boolean) - Constructor for class bacnet.expressionAtlas.core.GenomeElementAtlas: For a specific sequence update the list of BioCondition in which the genome element is over-expressed, under-expressed or not differently expressed
The update will be dependent of the value of the input filter = cutoff for LogFC and p-value
GenomeElements - Enum constant in enum bacnet.datamodel.dataset.OmicsData.ColNames
GenomeNCBI - Class in bacnet.datamodel.sequenceNCBI: Object containing an entire genome, created from NCBI RefSeq data
Data for this genome come from: NCBI.fna (for the sequence) NCBI.gff (for Gene, CDS, and ncRNA lists) If it exists some information are added: Rfam.gff (other info) supp info in a .txt file supp info about RAST results in a .txt file For EGD-e only: Srna.xml are read to add to the genome
GenomeNCBI() - Constructor for class bacnet.datamodel.sequenceNCBI.GenomeNCBI
GenomeNCBI(String, boolean) - Constructor for class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Create a genome with all chromosomes found If annotation = TRUE , we had the annotation we can found in other fasta files annotation = FALSE, we read only the complete genome + eventual plasmids
GenomeNCBIFolderTools - Class in bacnet.scripts.blast
GenomeNCBIFolderTools() - Constructor for class bacnet.scripts.blast.GenomeNCBIFolderTools
GenomeNCBITools - Class in bacnet.datamodel.sequenceNCBI
GenomeNCBITools() - Constructor for class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
GenomePhylogeny - Class in bacnet.scripts.phylogeny: Manage phylogeny from MLST scheme : Jolley and others
GenomePhylogeny() - Constructor for class bacnet.scripts.phylogeny.GenomePhylogeny
GenomesCreation - Class in bacnet.scripts.database: List of tools available for genome creation
GenomesCreation() - Constructor for class bacnet.scripts.database.GenomesCreation
GenomesListeriomics - Class in bacnet.scripts.listeriomics
GenomesListeriomics() - Constructor for class bacnet.scripts.listeriomics.GenomesListeriomics
GenomeTranscriptomeView - Class in bacnet.genomeBrowser: Display on the genome viewer: expression of specific bioCond and the log of fold change
GenomeTranscriptomeView() - Constructor for class bacnet.genomeBrowser.GenomeTranscriptomeView
GenomicsView - Class in bacnet.sequenceTools
GenomicsView() - Constructor for class bacnet.sequenceTools.GenomicsView
GENormalization - Class in bacnet.scripts.core.normalization
GENormalization() - Constructor for class bacnet.scripts.core.normalization.GENormalization
get(int) - Method in class bacnet.datamodel.dataset.Tiling
get(int) - Method in class org.biojava3.core.sequence.views.WindowedSequence: Returns the window specified at the given index in offsets i.e. asking for position 2 in a moving window sequence of size 3 will get you the window starting at position 4.
get(int, int, boolean) - Method in class bacnet.datamodel.dataset.Tiling: read probe values between two positions in the genome
important: bpbegin < bpend
get(Object) - Method in class org.biojava3.core.util.SoftHashMap
get10403SOverlap() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap
get10403SSrnas() - Static method in class bacnet.datamodel.sequence.Srna: Return a list of all Srna in 10403S
get3UTRSequence(int) - Method in class bacnet.datamodel.sequence.Sequence: Get the nucleotide sequence n bp downstream to the Sequence, +3bp for including start codon
getAAcidColor(String, Display) - Static method in class bacnet.datamodel.sequence.CompoundColorization: Given an Amino Acid, this method return the corresponding color
getAccession() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getAccession() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getAccession() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getAccession() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
getAccession() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getAccession() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
getAccession() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getAccession() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Unsupoorted
getAccession() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getAccession() - Method in interface org.biojava3.core.sequence.template.Accessioned: Returns the AccessionID this location is currently bound with
getAccession() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getAlias() - Method in class bacnet.datamodel.annotation.RfamElement
getAlignedSequence(int) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Uses bioIndex starting at 1 instead of 0
getAlignedSequence(int) - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns Sequence at given index.
getAlignedSequences() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Get the list of sequences
getAlignedSequences() - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns a List containing the individual Sequences of this alignment.
getAllAccession(ArrayList<BlastResult>) - Static method in class bacnet.scripts.blast.BlastResult: Return a list of all accessions contain in this list of results
getAllBioConditionNames() - Static method in class bacnet.datamodel.expdesign.BioCondition: Get all available BioCondition names by reading the text file Experiment.INCLUDE_COND_PATH
getAllBioConditions() - Method in class bacnet.Database
getAllBioConditions() - Static method in class bacnet.datamodel.expdesign.BioCondition: Return all BioCondition available
getAllButtons() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getAllButtons() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
getAllButtons() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getAllCodons() - Static method in class bacnet.datamodel.sequence.Codon: Return a TreeSet containing all possible codons
getAllCompounds() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
getAllCompounds() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
getAllCompounds() - Method in interface org.biojava3.core.sequence.template.CompoundSet
getAllElementNames() - Method in class bacnet.datamodel.sequence.Genome: Return all element names contained in all chromosomes
getAllElements() - Method in class bacnet.datamodel.sequence.Chromosome
getAllElements() - Method in class bacnet.datamodel.sequence.Genome: Return all elements contained in all chromosomes
getAllFrames() - Static method in enum org.biojava3.core.sequence.transcription.Frame: Delegates to Frame.values()
getAlllocusTag() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics
getAlllocusTagFromGFF() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics: They used old_locus_tag for the conservation analysis, so we need to create a HashMap to have the equivalent GeneId old_locus_tag ---> locus_tag in the GFF
getAlllocusTagINRA() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics
getAllPeptides(String, ArrayList<Integer>, ArrayList<String>, char, String, int, boolean, int) - Static method in class bacnet.scripts.blast.ProteinTools: Given a genome sequence, and a list of position of start codon, update a list of peptides accordingly
The new peptide, are the peptide from a start codon to the next R or stop codon
getAllPeptides(String, ArrayList<Integer>, ArrayList<String>, char, String, int, boolean, int) - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: Given a genome sequence, and a list of position of start codon, update a list of peptides accordingly
The new peptide, are the peptide from a start codon to the next R or stop codon
getAllPublishedBioConditions() - Static method in class bacnet.datamodel.expdesign.BioCondition: Return all BioCondition available
getAlltechnology() - Static method in class bacnet.scripts.arrayexpress.ArrayExpressTechnology: Go through all SDRF files and read the "Array Design REF" entry, save in ListTechno.txt
getAlltechnology() - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology: Go through all SDRF files and read the "Array Design REF" entry, save in ListTechno.txt
getAllUnPublishedBioConditions() - Static method in class bacnet.datamodel.expdesign.BioCondition: Return all BioCondition available
getAmbiguity(NucleotideCompound...) - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet: Calculates the best symbol for a collection of compounds.
getAminoAcid() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getAminoAcid(String) - Static method in class bacnet.datamodel.sequence.Codon: Translate a codon
getAminoAcidCharge(String) - Static method in class bacnet.datamodel.sequence.Codon: Using aminoacidCharge array, return the value of the charge for each amino acid aminoacidCharge = {{"R","1"},{"H","1"},{"K","1"},{"D","-1"},{"E","-1"}} else =0
getAminoAcidCompounds() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getAminoAcidCompoundSet() - Static method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
getANALYSIS_PATH() - Static method in class bacnet.Database
getAnnotation() - Method in class bacnet.datamodel.annotation.Annotation
getAnnotation() - Method in class bacnet.datamodel.dataset.NTermData
getAnnotation() - Method in class bacnet.datamodel.sequence.Chromosome
getAnnotation() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getAnnotation() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getANNOTATIONDATA_PATH() - Static method in class bacnet.Database
getAnnotationGenes(Genome, ArrayList<String>) - Static method in class bacnet.datamodel.annotation.Annotation: Extract a String[][] with all gene annotation information
getAnnotationMatrix(Genome) - Static method in class bacnet.datamodel.annotation.Annotation: Return a matrix containing different information on each element of the genome first chromosome
getAnnotationMatrix(Genome, ArrayList<String>) - Static method in class bacnet.datamodel.annotation.Annotation: Return a matrix containing different information on each element of the genome first chromosome
getAnnotations() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getAnnotationType() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getAnnotElementHeight() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getAnnotNumber() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getAnnotSeparationHeight() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getAnnotSeparationNumber() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getAntiComparisons() - Method in class bacnet.datamodel.expdesign.BioCondition
getAntiSDBindingFreeEnergy() - Method in class bacnet.datamodel.proteomics.NTerm
getArray() - Method in class bacnet.sequenceTools.SrnaSummaryView
getArrayDataList() - Method in class bacnet.sequenceTools.GeneView
getArrayDataList() - Method in class bacnet.sequenceTools.SrnaView
getArrayDesignRef(String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Read the SDRF table and search for the "Array Design REF" column
getArrayDesignRef(String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Read the SDRF table and search for the "Array Design REF" column
getArrayExpressArrayLink(String) - Static method in class bacnet.utils.RWTUtils
getArrayExpressExpLink(String) - Static method in class bacnet.utils.RWTUtils: Get ArrayExpress database link to a specific project
getArrayExpressId() - Method in class bacnet.datamodel.expdesign.BioCondition
getArrayExpressTechnoId() - Method in class bacnet.datamodel.expdesign.BioCondition
getArrayGeneToLocalization() - Method in class bacnet.sequenceTools.GeneView
getArrayProteomeList() - Method in class bacnet.sequenceTools.GeneView
getArrayTranscriptomesList() - Method in class bacnet.sequenceTools.GeneView
getAsList() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getAsList() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getAsList() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getAsList() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getAsList() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns this Sequence store as a List
getAsList() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getAsList() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Delegates to SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
getAsList() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getAsList() - Method in interface org.biojava3.core.sequence.template.Sequence: Returns the Sequence as a List of compounds
getAsList() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getAsRNAListEGDe() - Method in class bacnet.Database
getAsRNAs() - Method in class bacnet.datamodel.sequence.Chromosome
getAsRNAs() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getAsRNAs() - Method in class bacnet.datamodel.sequence.Genome: Return all AsRNas in all chromosomes
getAtisBHI(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: Go through all MassSpec data and find if the lmio was detected
getAtisBlood(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat
getaTISCutoff() - Method in class bacnet.datamodel.proteomics.NTermFilter
getaTISMap() - Method in class bacnet.datamodel.dataset.NTermData
getAttribute(String) - Method in class org.biojava3.genome.parsers.gff.Feature: Get value of specified attribute key.
getAttribute(String) - Method in interface org.biojava3.genome.parsers.gff.FeatureI: Get the attribute value for this key.
getAttributeOld(String) - Method in class org.biojava3.genome.parsers.gff.Feature
getAUNumber(String) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: Count the number of A and T nucleotides
getAvailableGenome() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
getAvailableGenome(boolean) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
getAvailableGenomes() - Static method in class bacnet.datamodel.sequence.Genome: Read a text file containing the different genome ID available for Listeria
getAWTColor(Color) - Static method in class bacnet.utils.BasicColor: Transform SWT color to AWT color
getBacillusGenome() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Return a list of all NON Listeria genomes
getBackingSequence() - Method in class org.biojava3.core.sequence.views.WindowedSequence: Access the sequence which backs this window
getBase() - Method in class org.biojava3.core.sequence.template.AbstractCompound
getBegin() - Method in class bacnet.datamodel.annotation.RfamElement
getBegin() - Method in class bacnet.datamodel.sequence.Sequence
getBegin() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
getBegin() - Method in class org.biojava3.genome.parsers.gff.Location
getBeginColumn() - Static method in class bacnet.datamodel.annotation.Annotation: Return the column index corresponding to Begin
getBioBegin() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getBioCondition() - Method in class bacnet.datamodel.dataset.ExpressionData: Return corresponding BioCondition
getBioCondition(String) - Static method in class bacnet.datamodel.expdesign.BioCondition: From a biological condition name load the corresponding BioCondition object
getBioCondition(String, boolean) - Static method in class bacnet.datamodel.expdesign.BioCondition: From a biological condition name, get from the ModelProvider the corresponding BioCondition object
If not available it will load them for the hard drive
getBIOCONDITION_PATH() - Static method in class bacnet.Database
getBioConditionHashMaps() - Method in class bacnet.genomeBrowser.core.DataTrack
getBioconditions() - Method in class bacnet.scripts.database.DataValidation
getBioConditions() - Method in class bacnet.datamodel.expdesign.Experiment
getBioConditions() - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
getBioConditions() - Method in class bacnet.scripts.core.Expression
getBioConditionsArrayPath() - Method in class bacnet.Database
getBioCondMax(String) - Method in class bacnet.genomeBrowser.core.DataTrack
getBioCondMin(String) - Method in class bacnet.genomeBrowser.core.DataTrack
getBioCondName() - Method in class bacnet.datamodel.dataset.OmicsData
getBioConds() - Method in class bacnet.datamodel.expdesign.Experiment
getBioConds() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
getBioConds() - Method in class bacnet.expressionAtlas.ProteomicsView
getBioConds() - Method in class bacnet.expressionAtlas.TranscriptomicsView
getBioConds() - Method in class bacnet.genomeBrowser.NTerminomicsView
getBioConds() - Method in class bacnet.sequenceTools.AnnotationView
getBioConds() - Method in class bacnet.sequenceTools.GeneView
getBioCondsArray() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
getBioCondsArray() - Method in class bacnet.expressionAtlas.ProteomicsView
getBioCondsArray() - Method in class bacnet.expressionAtlas.TranscriptomicsView
getBioCondsArray() - Method in class bacnet.genomeBrowser.NTerminomicsView
getBioCondsArray() - Method in class bacnet.sequenceTools.AnnotationView
getBioCondsArray() - Method in class bacnet.sequenceTools.GeneView
getBioCondsArray() - Method in class bacnet.sequenceTools.GenomicsView
getBioCondSize(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the size ratio that have a given BioCondition
getBioCondsToDisplay() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
getBioCondsToDisplay() - Method in class bacnet.expressionAtlas.ProteomicsView
getBioCondsToDisplay() - Method in class bacnet.expressionAtlas.TranscriptomicsView
getBioCondsToDisplay() - Method in class bacnet.genomeBrowser.NTerminomicsView
getBioCondsToDisplay() - Method in class bacnet.sequenceTools.AnnotationView
getBioCondsToDisplay() - Method in class bacnet.sequenceTools.GeneView
getBioCondsToDisplay() - Method in class bacnet.sequenceTools.GenomicsView
getBioEnd() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getBioEnd() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getBioEnd() - Method in interface org.biojava3.core.sequence.template.SequenceView: 1-indexed, inclusive.
getBioStart() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getBioStart() - Method in interface org.biojava3.core.sequence.template.SequenceView: 1-indexed, inclusive.
getBLAST_RESULT_PATH() - Static method in class bacnet.scripts.blast.Blast
getBlastDBInfo(String) - Static method in class bacnet.scripts.blast.Blast
getBlastExtension() - Static method in class bacnet.scripts.database.HomologCreation
getBlastFolder() - Static method in class bacnet.scripts.blast.Blast
getBlastFolder() - Static method in class bacnet.scripts.database.HomologCreation
getBlue() - Method in class bacnet.table.core.ColorSWT
getBodyFont(int) - Static method in class bacnet.swt.SWTResourceManager: Get the DEFAULT Font with appropriate height and style
getBodyFont(int, int) - Static method in class bacnet.swt.SWTResourceManager: Get the DEFAULT Font with appropriate height and style
getBoldFont(Font) - Static method in class bacnet.swt.SWTResourceManager: Returns a bold version of the given Font.
getBpSizeH() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getBpSizeH() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getBtnAllMutant() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
getBtnAllMutant() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnChooseOneMutant() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
getBtnChooseOneMutant() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnDeath() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnDnDNA() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnDnProt() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnDnRNA() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnExponential() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnGeneExpression() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnLagPhase() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnNoDNA() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnNoneMutant() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
getBtnNoneMutant() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnNoProt() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnNoRNA() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnOpenStructure() - Method in class bacnet.sequenceTools.SrnaView
getBtnPosDNA() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnPrint() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnRegrowth() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnRiboSeq() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnRnaseq() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnStationnary() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnSurvival() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnTermSeq() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnTiling() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnTss() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnUnpublished() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getBtnUpdateCutoff() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnUpProt() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnUpRNA() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getBtnZoomIn() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getBtnZoomInVertical() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getBtnZoomOut() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getBtnZoomOutVertical() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getBufferedReader() - Method in class org.biojava3.core.sequence.io.util.ClasspathResource: Returns the reader representation of this classpath resource
getBytesRead() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead: Keep track of bytesread via ReadLine to account for CR-LF in the stream.
getCAI(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: After generating TIRSequence.fasta in setTIRSequence() method we submit to http://genomes.urv.cat/CAIcal/ to calculate CAI value and expected CAI value The table with CAI values is saved from the website in: CAIResults.excel
getCAIGene(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: After generating GeneSequence.fasta in setGeneSequence() method we submit to http://genomes.urv.cat/CAIcal/ to calculate CAI value and expected CAI value The table with CAI values is saved from the website in: StatGenes/CAIGeneResults.excel
getCanvasData() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getCanvasGenome() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getCanvasName() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getCDSSequences() - Method in class org.biojava3.core.sequence.TranscriptSequence: Get the CDS sequences that have been added to the TranscriptSequences
getCenterColor() - Method in class bacnet.table.core.ColorMapper
getCenterColor() - Method in class bacnet.table.core.ColorMapperRCP
getCenterColorSWT() - Method in class bacnet.table.core.ColorMapper
getCenterColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getCenterPos() - Method in class bacnet.table.core.ColorMapper
getCenterPos() - Method in class bacnet.table.core.ColorMapperRCP
getCgview() - Method in class bacnet.scripts.genome.CircularGenomeJPanel
getChargedResidues(Gene, int) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: Sum up the different charge of the amino acids of the TIR
getChargedResiduesGene(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: Sum up the different charge of the amino acids of the gene sequence
getChildrenFeatures() - Method in class org.biojava3.core.sequence.features.AbstractFeature: Get the children features
getChildrenFeatures() - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Get the features contained by this feature
getChromoId() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
getChromoID() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getChromosome() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getChromosome() - Method in class bacnet.datamodel.sequence.Sequence: Return corresponding Chromosome given by this.getChromosomeNb
Load it if necessary
getChromosome() - Method in class bacnet.genomeBrowser.core.Track
getChromosomeFromDNASequence(LinkedHashMap<String, DNASequence>, Genome, int, String) - Static method in class bacnet.datamodel.sequence.Chromosome
getChromosomeID() - Method in class bacnet.datamodel.annotation.Annotation
getChromosomeID() - Method in class bacnet.datamodel.dataset.ExpressionData
getChromosomeID() - Method in class bacnet.datamodel.sequence.Chromosome
getChromosomeID() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getChromosomeID() - Method in class bacnet.datamodel.sequence.Sequence
getChromosomeID() - Method in class bacnet.genomeBrowser.core.Track
getChromosomeNames() - Method in class bacnet.datamodel.sequence.Genome: Get an ordered list of all chromosomes The order is fixed by the order of the chromosomes in the FNA (fasta) file used for reading the genome
getChromosomeNumber() - Method in class org.biojava3.core.sequence.ChromosomeSequence
getChromosomes() - Method in class bacnet.datamodel.sequence.Genome
getChromosomes() - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava3.genome.GeneFeatureHelper
getCisRegRNAListEGDe() - Method in class bacnet.Database
getCisRegs() - Method in class bacnet.datamodel.sequence.Chromosome
getCisRegs() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getCisRegs() - Method in class bacnet.datamodel.sequence.Genome: Return all CisRegs in all chromosomes
getCmbChromo() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
getCmbGenome() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
getCodingRegion(String) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence: Get the gene based on accession.
getCodingSequence() - Method in class org.biojava3.core.sequence.CDSSequence: A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence.
getCodingSequenceHashMap() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getCodingSequencesList(boolean) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Put in a list all the CodingSequence found
getCodonColor(double) - Method in class bacnet.datamodel.annotation.CodonUsage
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable: Returns the compound set of codons
getCodonCompoundSet(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava3.core.sequence.transcription.Table
getCodonProportion(Genome, String) - Static method in class bacnet.datamodel.sequence.Codon: Go through genome on both strand and calculate the proportion of each codon
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable: Returns a list of codons where the source and target compounds are the same as those given by the parameters.
getCodons(CompoundSet<NucleotideCompound>, CompoundSet<AminoAcidCompound>) - Method in interface org.biojava3.core.sequence.transcription.Table
getCodonUsage() - Method in class bacnet.datamodel.proteomics.NTerm
getCodonUsage(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getCOEXPR_NETWORK_TRANSCRIPTOMES_PATH() - Static method in class bacnet.Database: Path for loading Transcriptomes matrix data showing Log(Fold Change) values
getCoExpressionGlobalMatrix(Genome) - Static method in class bacnet.datamodel.dataset.Network: Calculate all pearson correlation and put it in a list of network interactions
Remove correlation CORR_CUTOFF
Nedd to load: Database.COEXPR_NETWORK_TRANSCRIPTOMES_PATH+"_Temp_"+genome.getSpecies()
getCoExprNetworkArrayPath() - Method in class bacnet.Database
getCoExprNetworks() - Method in class bacnet.scripts.database.DataValidation
getCog() - Method in class bacnet.datamodel.sequence.Gene
getCOG(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getCogClassification(ExpressionMatrix, GenomeNCBI) - Static method in class bacnet.datamodel.annotation.COGannotation
getCOGDescription(String) - Static method in class bacnet.datamodel.annotation.COGannotation: Return the COG description corresponding to a specific COGid
getCOGExpression(ExpressionMatrix) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Summarize an ExpressionMatrix by regrouping the different genes (rows) by their COG functional categories
Averages on all the genes for each category are calculated.
getCOGMap() - Static method in class bacnet.datamodel.annotation.COGannotation: Return a map from COG ID to COG description
getCOGNumberEGDe() - Static method in class bacnet.datamodel.annotation.COGannotation: Return a map between cogID and the number of genes associated to this cog in EGD-e
getColor(int) - Static method in class bacnet.swt.SWTResourceManager: Returns the system Color matching the specific ID.
getColor(int, int, int) - Static method in class bacnet.swt.SWTResourceManager: Returns a Color given its red, green and blue component values.
getColor(RGB) - Static method in class bacnet.swt.SWTResourceManager: Returns a Color given its RGB value.
getColorBetween(double, double, double, Color, Color) - Method in class bacnet.table.core.ColorMapper
getColorBetween(double, double, double, Color, Color) - Method in class bacnet.table.core.ColorMapperRCP
getColorMapper() - Method in class bacnet.table.gui.ColorMapperWizard
getColorMapper() - Method in class bacnet.table.gui.ColorMapperWizardPage
getColorMapperList() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
getColorMappers() - Method in class bacnet.table.core.ColorMapperList
getColorMappers() - Method in class bacnet.table.core.ColorMapperRCPList
getColors(int) - Static method in class bacnet.utils.BasicColor
getColumn(double[][], int) - Static method in class bacnet.utils.ArrayUtils: Extract a Column from a Matrix
getColumn(int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getColumn(String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Extract the column at this position
getColumn(String[][], int) - Static method in class bacnet.utils.ArrayUtils
getColumn(String[][], String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Read the SDRF table and search for the corresponding column
getColumn(String[][], String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Read the SDRF table and search for the corresponding column
getColumnIndex(String[][], String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Return column Index of the column named columnHeader
getColumnIndex(String[][], String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Return column Index of the column named columnHeader
getColumnNames() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
getColumnNames() - Method in class bacnet.expressionAtlas.ProteomicsView
getColumnNames() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
getColumnNames() - Method in class bacnet.expressionAtlas.TranscriptomicsView
getColumnNames() - Method in class bacnet.genomeBrowser.NTerminomicsView
getColumnNames() - Method in class bacnet.sequenceTools.AnnotationView
getColumnNames() - Method in class bacnet.sequenceTools.GenomicsView
getColumnNames() - Method in class bacnet.table.core.ColorMapper
getColumnNames() - Method in class bacnet.table.core.ColorMapperRCP
getComboAbsoluteRelative() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getComboGenome() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
getComboGenome() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getComboGenome() - Method in class bacnet.sequenceTools.GeneView
getComboMutant() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
getComboMutant() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getComment() - Method in class bacnet.datamodel.expdesign.BioCondition
getComment() - Method in class bacnet.datamodel.sequence.Sequence
getComment(Gene) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: Return information about gene or iTIS
getComparisonDataNames() - Method in class bacnet.datamodel.expdesign.BioCondition: Get every names of the Comparison which can be found:
Tiling arrays Gene Expression arrays ExpressionMatrix
getComparisonNames() - Method in class bacnet.datamodel.expdesign.BioCondition: Return a list of all Comparisons: bioCondName vs comparisons.get(i)
getComparisons() - Method in class bacnet.datamodel.expdesign.BioCondition
getComparisons() - Method in class bacnet.scripts.database.DataValidation
getCompExpression() - Method in class bacnet.scripts.core.Comparison
getCompFilter() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getComplement() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
getComplement() - Method in class org.biojava3.core.sequence.DNASequence: Returns a Sequence which will complement every base
getComplement() - Method in class org.biojava3.core.sequence.RNASequence: Get the complement view of the RNA sequence
getComplement() - Method in interface org.biojava3.core.sequence.template.ComplementCompound
getCompleteGenome(ArrayList<String>) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Extract all complete genomes from genomesList
getComposite() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getComposite_2() - Method in class bacnet.sequenceTools.SrnaView
getComposite_6() - Method in class bacnet.sequenceTools.SrnaView
getComposite_7() - Method in class bacnet.sequenceTools.SrnaView
getCompositeAddData() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getCompositeDataFilter() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
getCompositeDataFilter() - Method in class bacnet.expressionAtlas.ProteomicsView
getCompositeDataFilter() - Method in class bacnet.expressionAtlas.TranscriptomicsView
getCompositeNterm() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getCompositeSummary() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getCompositeTypeDisplay() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getComposition(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Does a linear scan over the given Sequence and records the number of times each base appears.
getCompoundAt(int) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getCompoundAt(int) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getCompoundAt(int) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns the compound at the specified biological index
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns the compound at the specified biological index
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getCompoundAt(int) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Always returns the compound given at construction
getCompoundAt(int) - Method in class org.biojava3.core.sequence.template.AbstractSequence
getCompoundAt(int) - Method in interface org.biojava3.core.sequence.template.Sequence: Returns the Compound at the given biological index
getCompoundAt(int) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getCompoundAt(int) - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
getCompoundAt(int) - Method in class org.biojava3.core.sequence.views.ReversedSequenceView
getCompoundAt(int) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
getCompoundForString(String) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
getCompoundForString(String) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
getCompoundForString(String) - Method in interface org.biojava3.core.sequence.template.CompoundSet: Return null if not recognised.
getCompounds(int) - Method in class org.biojava3.core.sequence.views.WindowedSequence: For a given position into the windowed view this will return those compounds we can see in the window. i.e. in the sequence AGGCCT requesting index 1 returns AGG and requesting index 2 return CCT.
getCompoundsAt(int) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Get a list of compounds at a sequence position
getCompoundsAt(int) - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns the Compound elements of the original Sequences at the given column.
getCompoundSet() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompound
getCompoundSet() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getCompoundSet() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getCompoundSet() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getCompoundSet() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Get the Compounds defined in the first sequence
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker: Returns the compound set backing this store
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns the compound set backing this store
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getCompoundSet() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Returns the compound set given at construction
getCompoundSet() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getCompoundSet() - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns CompoundSet of all Sequences
getCompoundSet() - Method in interface org.biojava3.core.sequence.template.Sequence: Gets the compound set used to back this Sequence
getCompoundSet() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getConservation() - Method in class bacnet.datamodel.sequence.Sequence
getConservationHashMap() - Method in class bacnet.datamodel.sequence.Sequence: Get HashMap linking genomeName to conserved gene
Give information about the genome in which this gene is conserved
getConsituents() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
getContainer() - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
getConvertPATH() - Static method in class bacnet.utils.ImageMagick: Need to convert path from local use or server utilization
getCorrespondingMapper(String) - Method in class bacnet.table.core.ColorMapperList
getCorrespondingMapper(String) - Method in class bacnet.table.core.ColorMapperRCPList
getCreator() - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
getCurrentState() - Method in class bacnet.Database
getCursor(int) - Static method in class bacnet.swt.SWTResourceManager: Returns the system cursor matching the specific ID.
getCutOff1() - Method in class bacnet.table.core.Filter
getCutOff1() - Method in class bacnet.utils.Filter
getCutOff2() - Method in class bacnet.table.core.Filter
getCutOff2() - Method in class bacnet.utils.Filter
getCutoffHashMap() - Method in class bacnet.datamodel.proteomics.NTermFilter
getDATA_PATH() - Static method in class bacnet.Database: GETTER AND SETTERS
getDatabase() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
getDatabaseFeatures() - Method in class bacnet.Database
getDatabaseReferences() - Method in interface org.biojava3.core.sequence.features.DatabaseReferenceInterface
getDatabaseReferences() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: The Uniprot mappings to other database identifiers for this sequence
getDatabaseReferences() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getDataColors() - Method in class bacnet.genomeBrowser.core.DataTrack
getDataCount() - Method in class bacnet.genomeBrowser.core.DataTrack: Count the number of data available, without duplicate and filtered
getDataDisplayed() - Method in class bacnet.genomeBrowser.core.DataTrack: Get the list of data to display
getDataDisplayedNames() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the names of the data which will be displayd
getDataFromLab() - Static method in class bacnet.scripts.database.TranscriptomesCreation: Get all GeneExpression from the lab
getDataNames() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of all the data available
getDataNOTDisplayed() - Method in class bacnet.genomeBrowser.core.DataTrack
getDataRegion() - Method in class bacnet.genomeBrowser.core.Track
getDatas() - Method in class bacnet.genomeBrowser.core.Track
getDatasets() - Method in class bacnet.datamodel.dataset.NGS
getDataSize() - Method in class bacnet.genomeBrowser.core.DataTrack
getDataSizes() - Method in class bacnet.genomeBrowser.core.DataTrack
getDataSource() - Method in class org.biojava3.core.sequence.AccessionID
getDataSource() - Method in class org.biojava3.core.sequence.location.InsdcParser
getDataSource() - Method in class org.biojava3.core.sequence.TaxonomyID
getDataTotalSize(Track.DisplayType) - Method in class bacnet.genomeBrowser.core.DataTrack: Add all the size of the Tracks to know the total size of the display window
getDataWindowSize() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getDate() - Method in class bacnet.datamodel.dataset.OmicsData
getDate() - Method in class bacnet.datamodel.expdesign.BioCondition
getDbxref(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getDecaySliderVBar() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getDefault() - Static method in class org.biojava3.core.sequence.transcription.TranscriptionEngine: Default instance to use when Transcribing from DNA -> RNA -> Protein.
getDefaultFrame() - Static method in enum org.biojava3.core.sequence.transcription.Frame
getDefautGenome() - Static method in class bacnet.datamodel.sequence.Genome: Return defaut genome for a databse
For the moment -> first element of getAvailableGenomes()
getDescription() - Method in class bacnet.datamodel.annotation.Signature
getDescription() - Method in class org.biojava3.core.sequence.compound.CodonCompound
getDescription() - Method in class org.biojava3.core.sequence.features.AbstractFeature
getDescription() - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Get the description that can be used to describe the feature
getDescription() - Method in class org.biojava3.core.sequence.template.AbstractCompound
getDescription() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getDescription() - Method in interface org.biojava3.core.sequence.template.Compound
getDescription() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
getDescription() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getDetectable(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: By reading the List in: /StatGenes/EGDeDetectable.txt Say if a gene is detectable by the spectometer or not
getDeviation() - Method in class bacnet.table.core.ColorMapper
getDeviation() - Method in class bacnet.table.core.ColorMapperRCP
getDeviation(ArrayList<Tiling>, String) - Static method in class bacnet.datamodel.dataset.Tiling: Calculate the stat deviation on each probe of a list of Tiling
getDirection() - Method in class bacnet.table.core.BioConditionComparator
getDirection() - Method in class bacnet.table.core.TableViewerComparator
getDisplay() - Method in class bacnet.genomeBrowser.core.DataTrack
getDisplay() - Method in class bacnet.table.core.ColorMapper
getDisplayRegion() - Method in class bacnet.genomeBrowser.core.Track
getDisplayType() - Method in class bacnet.genomeBrowser.core.Track
getDistribution(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Analogous to SequenceMixin.getComposition(Sequence) but returns the distribution of that Compound over the given sequence.
getDNACodingSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence: Get the stitched together CDS sequences then maps to the cDNA
getDNACodingSequences() - Method in class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
getDnaCompounds() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getDNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
getDNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.AmbiguityRNACompoundSet
getDNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.DNACompoundSet
getDnaRnaTranslator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getDNASeqDatas() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of SeqDatas
getDNASeqDatas(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of RiboSeqData given a bioCondName
getDnaToRna() - Method in class org.biojava3.core.sequence.views.RnaSequenceView
getDNAType() - Method in class org.biojava3.core.sequence.DNASequence
getDownDNAList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getDownloadLink() - Method in class bacnet.views.InternalBrowser
getDownloadUrl(String, File, EPartService) - Static method in class bacnet.raprcp.DownloadServiceHandler
getDownloadUrl(String, String, EPartService) - Static method in class bacnet.raprcp.DownloadServiceHandler
getDownProtList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getDownRNAList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getDuplicates() - Method in class bacnet.datamodel.proteomics.NTerm
getDuplicateSequenceToRemove() - Method in class bacnet.datamodel.proteomics.NTermFilter
getEdges() - Method in class bacnet.datamodel.dataset.Network: An hashMap which map each vertex (=genome element) to the correlated vertex.
Vertex -> HashMap<Vetrex,PearsonCorrelation>
getEGDcOverlap() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap
getEGDcSrnas() - Static method in class bacnet.datamodel.sequence.Srna: Return a list of all Srna in EGD-c
getEGDe() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Read RAST automoticaly annotated EGD-e genome
getEGDeALLSrnas() - Static method in class bacnet.datamodel.sequence.Srna: Return a list of all Srna, CisReg and ASrna in EGD-e
getEGDeAutoOverlap() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Go through EGDe overlap and find when two genes overlap
getEgdeOperonList() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversionElement
getEgdeOperonMap() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversionElement
getEGDeOverlap() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap
getEGDeRASTAutoOverlap() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Find RASt element which overlap another element in the genome
getEGDeSrnas() - Static method in class bacnet.datamodel.sequence.Srna: Return an ordered list of all Srna in EGD-e
getEGDeUnknownRAST() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap
getElement(String) - Method in class bacnet.datamodel.sequence.Genome: Search an element by its name in the genome
getElementATbp(Chromosome, int) - Method in class bacnet.datamodel.annotation.Annotation: Return the first element for which
begin < bpPosition < end
getElementInfoATbp(Chromosome, int) - Method in class bacnet.datamodel.annotation.Annotation: Return the first element for which
begin < bpPosition < end
getElements() - Method in class bacnet.datamodel.annotation.Signature
getElements() - Method in class bacnet.datamodel.dataset.NTermData: Link NTerm name to NTerm
This correspond to the list of NTerm
getElements() - Method in class bacnet.datamodel.sequence.Chromosome
getElements() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getElements(Chromosome, int, int) - Method in class bacnet.datamodel.annotation.Annotation: Get the lists of elements between beginDraw and endDraw
getElementsToDisplay(int, int, String) - Method in class bacnet.datamodel.dataset.NTermData: Get the lists of NTerm between beginDraw and endDraw
getENALink(String) - Static method in class bacnet.utils.RWTUtils
getEnd() - Method in class bacnet.datamodel.annotation.RfamElement
getEnd() - Method in class bacnet.datamodel.sequence.Sequence
getEnd() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
getEnd() - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
getEnd() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
getEnd() - Method in interface org.biojava3.core.sequence.location.template.Location: End of the location
getEnd() - Method in class org.biojava3.genome.parsers.gff.Location
getEnd(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.Substitute: Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.
getEndColumn() - Static method in class bacnet.datamodel.annotation.Annotation: Return the column index corresponding to End
getEntry(String, String) - Method in interface bacnet.swt.ResourceManager.PluginResourceProvider
getEquivalentCompounds(C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
getEquivalentCompounds(C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
getEquivalentCompounds(AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
getExcludeColumn() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
getExcludeColumn() - Method in class bacnet.table.core.Filter
getExcludeColumn() - Method in class bacnet.table.core.FilterList
getExcludeColumn() - Method in class bacnet.utils.Filter
getExcludeRow() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
getExcludeRow() - Method in class bacnet.table.core.Filter
getExcludeRow() - Method in class bacnet.table.core.FilterList
getExcludeRow() - Method in class bacnet.utils.Filter
getExcludeRows() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getExonSequences() - Method in class org.biojava3.core.sequence.GeneSequence: Get the exons as an ArrayList
getExperienceNb() - Method in class bacnet.datamodel.expdesign.BioCondition
getExperiment() - Method in class bacnet.datamodel.proteomics.NTerm: Return if the NTerm was detected in the first experiment, or the second, or both
getExperiment() - Method in class bacnet.datamodel.proteomics.TIS: Return if the NTerms of this TIS were detected in the first experiment, or the second, or both
getExperimentComparisonTablePath() - Method in class bacnet.Database
getExpression() - Method in class bacnet.scripts.core.Comparison
getExpression() - Method in class bacnet.scripts.core.Expression
getEXPRESSION_MATRIX_PROTEOMES_PATH() - Static method in class bacnet.Database: Path for loading Proteomes matrix data showing absolute expression values
getEXPRESSION_MATRIX_TRANSCRIPTOMES_PATH() - Static method in class bacnet.Database: Path for loading Transcriptomes matrix data showing expression values
getExpressionData() - Method in class bacnet.datamodel.expdesign.BioCondition: Put all ExpressionData in a list
getExpressionMatrix(double[][]) - Static method in class bacnet.scripts.core.stat.AMtools
getExprProteomesTable() - Method in class bacnet.Database
getExprProteomesTable(String) - Method in class bacnet.Database
getExprTranscriptomesTable() - Method in class bacnet.Database
getExprTranscriptomesTable(String) - Method in class bacnet.Database
getExtension() - Static method in class bacnet.datamodel.dataset.ExpressionData
getExtension() - Static method in class bacnet.datamodel.dataset.OmicsData
getExtension(String) - Static method in class bacnet.utils.FileUtils: Get the extension in a fileName
getFAAPath(String) - Static method in class bacnet.scripts.database.HomologCreation
getFeature(String) - Method in class bacnet.datamodel.sequence.Sequence: Get the feature in the HashMap, pointed by the key attribute
return "" if not found
getFeatures() - Method in class bacnet.datamodel.sequence.Sequence
getFeatures() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getFeatures(int) - Method in class org.biojava3.core.sequence.template.AbstractSequence: Return features at a sequence position
getFeatures(String, int) - Method in class org.biojava3.core.sequence.template.AbstractSequence: Return features at a sequence position by type
getFeaturesByType(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
getFeaturesKeyWord() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getFeaturesText() - Method in class bacnet.datamodel.sequence.Sequence: Create a String containing all features and their attribute
getFeaturesTextForTable(String) - Method in class bacnet.datamodel.sequence.Sequence: Used when displaying information in SrnaView
Display only supplementary information of each Srna publication
getFile() - Method in class bacnet.raprcp.DownloadServiceHandler
getFileBytes(File) - Static method in class bacnet.utils.FileUtils
getFileName() - Method in class bacnet.raprcp.DownloadServiceHandler
getFileName() - Method in class bacnet.views.InternalBrowser
getFilteredNetwork() - Method in class bacnet.e4.rap.SynTView
getFilteredNetwork() - Method in class bacnet.views.CoExprNetworkView
getFilters() - Method in class bacnet.table.core.FilterList
getFirstChromosome() - Method in class bacnet.datamodel.sequence.Genome: Get the first chromosome in the HashMap Is Used to replace: Genome.loadGenome(genomeName).getChromosomes().get(0)
getFirstChromosome() - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Get the first chromosome in the HashMap Is Used to replace: GenomeNCBI.getChromosomes().get(0)
getFirstCodon(Sequence) - Static method in class bacnet.datamodel.sequence.Codon: Return first threee nucleotide of a Sequence
getFirstMapper() - Method in class bacnet.table.core.ColorMapperList
getFirstMapper() - Method in class bacnet.table.core.ColorMapperRCPList
getFirstRowName() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getFont(String, int, int, boolean, boolean) - Static method in class bacnet.swt.SWTResourceManager: Returns a Font based on its name, height and style.
getFontDouble() - Method in class bacnet.table.core.ColorMapper
getFontDouble() - Method in class bacnet.table.core.ColorMapperRCP
getFontRowName() - Method in class bacnet.table.core.ColorMapper
getFontString() - Method in class bacnet.table.core.ColorMapperRCP
getFontText() - Method in class bacnet.table.core.ColorMapper
getFormylatedExperiment() - Method in class bacnet.datamodel.proteomics.TIS: Search if the TIS was found formylated in the first experiment, or the second, or both
getForwardFrames() - Static method in enum org.biojava3.core.sequence.transcription.Frame: Returns all frames in the forward orientation
getFoundIn() - Method in class bacnet.datamodel.sequence.Srna
getFoundInText() - Method in class bacnet.datamodel.sequence.Srna
getFromCompoundSet() - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
getFullORF(Sequence, Genome) - Static method in class bacnet.datamodel.proteomics.NTermUtils: Giving a position and a strand on the genome we extract the full ORF (in frame) containing the peptide (amino acid sequence)
getFullORF(String, int, int, boolean, Genome) - Static method in class bacnet.datamodel.proteomics.NTermUtils: Giving a position and a strand on the genome we extract the full ORF (in frame) containing the peptide (amino acid sequence)
getGC() - Method in class org.biojava3.core.sequence.RNASequence
getGCCount() - Method in class org.biojava3.core.sequence.DNASequence: Get the GC count in the DNA Sequence
getGCGChecksum(List<S>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Calculates GCG checksum for entire list of sequences
getGCGChecksum(S) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Calculates GCG checksum for a given sequence
getGCGHeader(List<S>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Assembles a GCG file header
getGCGType(CompoundSet<C>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Determines GCG type
getGCNumber(String) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: Count the number of G and C nucleotides
getGCStats(Collection<DNASequence>) - Static method in class org.biojava3.genome.parsers.gff.GCStats
getGCStatsString(Collection<String>) - Static method in class org.biojava3.genome.parsers.gff.GCStats
getGene(String) - Method in class org.biojava3.core.sequence.ChromosomeSequence: Get the gene based on accession.
getGene(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getGeneDownstream() - Method in class bacnet.datamodel.sequence.Gene: Return the gene downstream on the + strand
getGeneDownstream(Gene) - Method in class bacnet.datamodel.sequence.Chromosome: Return the gene downstream
getGeneExpr() - Static method in class bacnet.datamodel.dataset.EGDeWTdata: Read GeneEpression corresponding to NAME_Mean, and return it
getGeneExpr(Gene, String) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: Return the median value expression (calculated on 10 BHI 37C data) in the Gene Expression array of the gene
getGeneExprs() - Method in class bacnet.datamodel.expdesign.BioCondition
getGeneExprs() - Method in class bacnet.datamodel.expdesign.Experiment: Return all GeneExpression data contains in all BioCondition
getGeneExprs() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of GeneExpressions
getGeneExprs(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of GeneExpression given a bioCondName
getGeneFromName(String) - Method in class bacnet.datamodel.sequence.Genome: Go through all chromosomes and each Genes map and GeneName map to find the corresponding gene
getGeneFromName(String) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Go through codingSequence and nonCodingSequence searching for corresponding accession or locus
getGeneFromName(String, String) - Method in class bacnet.datamodel.sequence.Genome: Go through all chromosomes and each Genes map and GeneName map to find the corresponding gene
getGeneFromProteinId(String) - Method in class bacnet.datamodel.sequence.Genome: Go through all chromosomes and Gene from corresponding proteinid
getGeneListEGDe() - Method in class bacnet.Database
getGeneModification() - Method in class bacnet.datamodel.dataset.NTermData
getGeneName() - Method in class bacnet.datamodel.sequence.Gene
getGeneName() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: Get the gene name associated with this sequence.
getGeneName(String) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Look in LocusTagToGeneName if a geneName exists
getGeneNameList() - Method in class bacnet.datamodel.sequence.Chromosome: Return a List with all name of genes
getGeneNames() - Method in class bacnet.datamodel.sequence.Genome: Return all the Gene locus tag name available in every chromosome
getGeneNameToLocusTagMap() - Method in class bacnet.datamodel.sequence.Chromosome
getGeneNameToLocusTagMap() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getGeneralExp() - Static method in class bacnet.datamodel.expdesign.Experiment: Load all experiment
If all experiments are already loaded just get the general experiment found in ModelProvider.INSTANCE
getGeneralExperiment() - Method in class bacnet.Database
getGeneralNetwork() - Method in class bacnet.e4.rap.SynTView
getGeneralNetwork() - Method in class bacnet.views.CoExprNetworkView
getGeneralWtName() - Static method in class bacnet.datamodel.dataset.ExpressionData
getGenes() - Method in class bacnet.datamodel.dataset.NTermData
getGenes() - Method in class bacnet.datamodel.sequence.Chromosome
getGenes() - Method in class bacnet.datamodel.sequence.Genome: Return all Genes in all chromosomes
getGenes() - Method in class bacnet.datamodel.sequence.Operon
getGenesAlternative() - Method in class bacnet.datamodel.sequence.Chromosome
getGeneSequences() - Method in class org.biojava3.core.sequence.ChromosomeSequence: Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key.
getGeneSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava3.genome.GeneFeatureHelper
getGeneToOperon() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversionElement
getGeneToSigMap(ChromosomeBacteriaSequence) - Static method in class bacnet.datamodel.annotation.Signature: Create a mapping between gene to a signature
All signatures from the folder Database.getSIGNATURES() are used
getGeneUpstream() - Method in class bacnet.datamodel.sequence.Gene: Return the gene upstream on the + strand
getGeneUpstream(Gene) - Method in class bacnet.datamodel.sequence.Chromosome: Return the gene upstream
getGenome() - Method in class bacnet.datamodel.annotation.Annotation
getGenome() - Method in class bacnet.datamodel.annotation.Signature
getGenome() - Method in class bacnet.datamodel.expdesign.BioCondition: Return corresponding Genome given by this.genomeName
Load it if necessary
getGenome() - Method in class bacnet.datamodel.sequence.Sequence: Return corresponding Genome given by this.genomeName
Load it if necessary
getGenome() - Method in class bacnet.scripts.core.Expression
getGenome() - Method in class bacnet.sequenceTools.AnnotationView
getGenome() - Method in class bacnet.sequenceTools.GeneView
getGenome() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
getGenome() - Method in class bacnet.sequenceTools.SrnaView
getGenome() - Method in class bacnet.views.CoExprNetworkView
getGenome(String) - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Read a genome from RAST results
getGenomeAA() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getGenomeAACompl() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getGenomeAAMinus() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getGenomeAAMinusCompl() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getGenomeAAPlus() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getGenomeAAPlusCompl() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getGenomeArrayPath() - Method in class bacnet.Database
getGenomeElements() - Method in class bacnet.scripts.core.Comparison
getGenomeElements() - Method in class bacnet.scripts.core.Expression
getGenomeList() - Method in class bacnet.Database
getGenomeName() - Method in class bacnet.datamodel.dataset.ExpressionData
getGenomeName() - Method in class bacnet.datamodel.dataset.NGS
getGenomeName() - Method in class bacnet.datamodel.expdesign.BioCondition
getGenomeName() - Method in class bacnet.datamodel.sequence.Sequence
getGenomeName() - Method in class bacnet.e4.rap.SynTView
getGenomeName() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getGenomeName() - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
getGenomeName() - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
getGenomeName() - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
getGenomeName() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
getGenomeName() - Method in class bacnet.genomeBrowser.core.Track
getGenomeName() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getGenomeName() - Method in class bacnet.views.CoExprNetworkView
getGenomeNCBILink(String) - Static method in class bacnet.utils.RWTUtils
getGenomes() - Method in class bacnet.Database
getGenomes() - Method in class bacnet.scripts.database.DataValidation: GETTER AND SETTER
getGenomes() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics: get the list of genome IDs and corresponding genome Names
And verify if all genomes are here!
getGENOMES_PATH() - Static method in class bacnet.Database
getGenomesAvalaible() - Static method in class bacnet.scripts.phylogeny.GenomePhylogeny: Create list of genomes which contains all genome available
This genome list contains all the genomes both from GenomeFolder and GenomePhylogeny.PATH_TABLE (=All bacteria phylogeny)
getGenomeSelected() - Method in class bacnet.sequenceTools.GeneView: The comboGenome contains modified genome name so we need this method to get selected element
a '*' is add to genome name when a transcriptome data is available
getGenomeSelected() - Method in class bacnet.views.CoExprNetworkView: The comboGenome contains modified genome name so we need this method to get selected element
a '*' is add to genome name when a transcriptome data is available
getGenomesNCBI() - Method in class bacnet.Database
getGenomeUsed() - Method in class bacnet.datamodel.expdesign.BioCondition
getGenomeViewerColumnIndex() - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Return the appropriate column index for displaying in the Genome viewer
By order of priority: LOGFC containing column FC containing column p-value containing column VALUE first column
getGExpressionData(ArrayList<String>) - Static method in class bacnet.datamodel.dataset.GeneExpression: List all TilingData available by biocondName.
getGExpressionData(ArrayList<String>, ArrayList<String>) - Static method in class bacnet.datamodel.dataset.GeneExpression: Load all Tiling present in leftBCs and rightBCs.
getGlaserFC(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getGlaserFCDescription(String) - Static method in class bacnet.datamodel.annotation.GlaserFCannotation: Return the Glaser Functional categories description corresponding to a specific glaserFCID
getGlaserFCMap() - Static method in class bacnet.datamodel.annotation.GlaserFCannotation: Return a map from glaserFCID to Glaser et al. 2001 Functional categories description
getGoogleId() - Method in class bacnet.Database
getGreen() - Method in class bacnet.table.core.ColorSWT
getGrowth() - Method in class bacnet.datamodel.expdesign.BioCondition
getHeader(int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getHeader(S) - Method in class org.biojava3.core.sequence.io.GenericFastaHeaderFormat
getHeader(S) - Method in interface org.biojava3.core.sequence.io.template.FastaHeaderFormatInterface
getHeaderAnnotation() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getHeaderColor() - Method in class bacnet.table.core.ColorMapperRCP
getHeaderColorSWT() - Method in class bacnet.table.core.ColorMapper
getHeaderColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getHeaders() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getHeadersListToArray() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getHeadersToArray() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getHeaderValues(String) - Method in class bacnet.reader.NCBIFastaHeaderParser: Parse out the components where some have a | and others do not
getHeight() - Method in class bacnet.genomeBrowser.core.Region
getHeight() - Method in class bacnet.table.core.MatrixSize
getHeightDefault() - Method in class bacnet.table.core.MatrixSize
getHeightPix() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getHeightPix() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getHitsQueryDef(double) - Method in class org.biojava3.genome.query.BlastXMLQuery
getHTMLVersion(Object[][]) - Static method in class bacnet.reader.TabDelimitedTableReader: Save the table in a text file containing an HTML table
getId() - Method in class bacnet.datamodel.annotation.RfamElement
getId() - Method in class bacnet.datamodel.sequence.Sequence
getId() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
getId() - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
getID() - Method in class bacnet.datamodel.annotation.Signature
getID() - Method in class org.biojava3.core.sequence.AccessionID
getID() - Method in class org.biojava3.core.sequence.TaxonomyID
getIDFormat(List<S>) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Creates format String for accession IDs
getIDFPath(String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Get path of IDF file for a specific dataID (ex: E-MTAB-1800)
getIDFPath(String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Get path of IDF file for a specific dataID (ex: E-MTAB-1800)
getImage(Class<?>, String) - Static method in class bacnet.swt.SWTResourceManager: Returns an Image stored in the file at the specified path relative to the specified class.
getImage(String) - Static method in class bacnet.swt.SWTResourceManager: Returns an Image stored in the file at the specified path.
getImage(ImageDescriptor) - Static method in class bacnet.swt.ResourceManager: Returns an Image based on the specified ImageDescriptor.
getImageChecked() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getImageDescriptor(Class<?>, String) - Static method in class bacnet.swt.ResourceManager: Returns an ImageDescriptor stored in the file at the specified path relative to the specified class.
getImageDescriptor(String) - Static method in class bacnet.swt.ResourceManager: Returns an ImageDescriptor stored in the file at the specified path.
getImageGeneExpr() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getImageRNASeq() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getImageTilingGeneExpr() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getImageTSS() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getImageTSSTilingGeneExpr() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getImageUnchecked() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getIndexOf(C) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getIndexOf(C) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getIndexOf(C) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns the first occurrence of the given compound in this store; performs a linear search
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getIndexOf(C) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Returns 1 if the given compound is equal to the one given during construction; otherwise will return -1.
getIndexOf(C) - Method in class org.biojava3.core.sequence.template.AbstractSequence
getIndexOf(C) - Method in interface org.biojava3.core.sequence.template.Sequence: Scans through the Sequence looking for the first occurrence of the given compound
getIndexOf(C) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getIndexOf(C) - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
getIndexOf(NucleotideCompound) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
getInfo() - Method in class bacnet.datamodel.sequence.Gene: Return a String containing getProduct() and getComment() information
getInHTML(String[][], String) - Static method in class bacnet.reader.TabDelimitedTableReader: Return an HTML version of the table
getInHTML(ArrayList<String>, String) - Static method in class bacnet.reader.TabDelimitedTableReader: Return an HTML version of the ArrayList
getInitView() - Method in class bacnet.Database
getInocuaColor(double) - Method in class bacnet.table.core.ColorMapper
getInocuaColor(double) - Method in class bacnet.table.core.ColorMapperRCP
getInputStream() - Method in class org.biojava3.core.sequence.io.util.ClasspathResource: Returns the InputStream instance of this classpath resource
getInputStream(File) - Method in class org.biojava3.core.util.InputStreamProvider: get an InputStream for the file
getInputStream(String) - Static method in class org.biojava3.core.util.FlatFileCache
getInputStream(String) - Method in class org.biojava3.core.util.InputStreamProvider: get an InputStream for this file
getInputStream(URL) - Method in class org.biojava3.core.util.InputStreamProvider
getInstance() - Static method in class bacnet.Database
getInstance() - Static method in class org.biojava3.core.sequence.io.IUPACParser
getInstance() - Static method in class org.biojava3.core.util.FlatFileCache
getIntronSequences() - Method in class org.biojava3.core.sequence.GeneSequence: Get the introns as an ArrayList
getInverse() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getInverse() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getInverse() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getInverse() - Method in class org.biojava3.core.sequence.RNASequence: Get the inverse view of the sequence.
getInverse() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getInverse() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
getInverse() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getInverse() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
getInverse() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getInverse() - Method in interface org.biojava3.core.sequence.template.Sequence: Does the right thing to get the inverse of the current Sequence.
getInverse() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getIsoelectricPoint(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getiTIS() - Method in class bacnet.scripts.listeriomics.nterm.NTermStat
getJeffInfo() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the different tables from Jeff summary table in 2011 and create a list of sRNAs from the different tables
getJohanssonInfo() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the table from Johansson 2009 data and create a list of sRNAs from the different tables
getJolleyIDtoInfo() - Static method in class bacnet.scripts.phylogeny.GenomePhylogeny: Map Jolley ID to corresponding row in PATH_INFOTABLE
getKeyWords() - Method in interface org.biojava3.core.sequence.features.FeaturesKeyWordInterface
getKeyWords() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: Pull uniprot key words which is a mixed bag of words associated with this sequence
getLabel_2() - Method in class bacnet.sequenceTools.SrnaView
getLabel_3() - Method in class bacnet.sequenceTools.SrnaView
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns the last occurrence of the given compound in this store; performs a linear search
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Returns the length of the Sequence if the given compound was equal to the one given during construction.
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.template.AbstractSequence
getLastIndexOf(C) - Method in interface org.biojava3.core.sequence.template.Sequence: Scans through the Sequence looking for the last occurrence of the given compound
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getLastIndexOf(C) - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
getLastIndexOf(NucleotideCompound) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
getLblDescribedIn() - Method in class bacnet.sequenceTools.SrnaView
getLblGene() - Method in class bacnet.sequenceTools.SrnaView
getLblNodiff() - Method in class bacnet.sequenceTools.GeneView
getLblNodiffProteome() - Method in class bacnet.sequenceTools.GeneView
getLblOrAnyOther() - Method in class bacnet.sequenceTools.SrnaView
getLblOver() - Method in class bacnet.sequenceTools.GeneView
getLblOverProteome() - Method in class bacnet.sequenceTools.GeneView
getLblOverProteomes() - Method in class bacnet.sequenceTools.GeneView
getLblOverTranscriptomes() - Method in class bacnet.sequenceTools.GeneView
getLblPredictedSecondaryStructure() - Method in class bacnet.sequenceTools.SrnaView
getLblStructure() - Method in class bacnet.sequenceTools.SrnaView
getLblTranscriptomesData() - Method in class bacnet.sequenceTools.GeneView
getLblUnder() - Method in class bacnet.sequenceTools.GeneView
getLblUnderProteome() - Method in class bacnet.sequenceTools.GeneView
getLeftBCs() - Method in class bacnet.scripts.core.Comparison
getLength() - Method in class bacnet.datamodel.dataset.ExpressionData
getLength() - Method in class bacnet.datamodel.sequence.Sequence
getLength() - Method in class org.biojava3.core.sequence.CDSSequence
getLength() - Method in class org.biojava3.core.sequence.ExonSequence
getLength() - Method in class org.biojava3.core.sequence.GeneSequence
getLength() - Method in class org.biojava3.core.sequence.IntronSequence
getLength() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getLength() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getLength() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: The sequence length
getLength() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
getLength() - Method in interface org.biojava3.core.sequence.location.template.Location: Returns the length of the outer bounds of this location
getLength() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Get the length of the MSA where it is assumed that all sequence position
getLength() - Method in class org.biojava3.core.sequence.StartCodonSequence
getLength() - Method in class org.biojava3.core.sequence.StopCodonSequence
getLength() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getLength() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
getLength() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns the length of the sequence
getLength() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getLength() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Returns the length given during construction
getLength() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getLength() - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns the number of columns in the alignment profile.
getLength() - Method in interface org.biojava3.core.sequence.template.Sequence: Returns the length of the Sequence
getLength() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getLength() - Method in class org.biojava3.core.sequence.TranscriptSequence
getLength() - Method in class org.biojava3.core.sequence.views.WindowedSequence: Returns the size of the windowed sequence which is the length by the window size.
getLength(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getLengthAA() - Method in class bacnet.datamodel.sequence.Gene
getLengthGenome() - Method in class bacnet.datamodel.sequence.Genome: Return the total length of the genome by adding all chromosomes lengths
getLengthProt(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getLineLength() - Method in class org.biojava3.core.sequence.io.FastaGeneWriter
getLineLength() - Method in class org.biojava3.core.sequence.io.FastaWriter
getLinkedBioCondition() - Method in class bacnet.datamodel.expdesign.BioCondition
getList() - Method in class org.biojava3.core.sequence.io.util.ClasspathResource: Returns this resource as a list of Strings
getList(BufferedReader) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Returns the contents of a buffered reader as a list of strings
getList(File) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Delegates to IOUtils.getList(InputStream) by wrapping the File in a valid stream.
getList(InputStream) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Delegates to IOUtils.getList(BufferedReader) by wrapping the InputStream in a valid reader.
getListData() - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Read DATA_TABLe and return the list of dataset IDs
getListData() - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Read DATA_TABLe and return the list of dataset IDs
getLISTDATA_COEXPR_NETWORK_TRANSCRIPTOMES_PATH() - Static method in class bacnet.Database: Path for loading Transcriptomes matrix data showing Log(Fold Change) values
getListDatabases() - Method in class bacnet.Database
getListeriaGenomes() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Return a List of all Listeria genomes available
getListeriaMonoGenome() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Return a List of all Listeria Monocytogenes genomes available
getListeriaNonMonoGenome() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Return a List of all Listeria NOT Monocytogenes genomes available
getListGenes() - Method in class bacnet.sequenceTools.GeneView
getListOfFullORFfromPeptide(String, Genome) - Static method in class bacnet.datamodel.proteomics.NTermUtils: From a list of peptide position retrieve the complete sequence of the ORF (in frame) containing the peptide (amino acid sequence)
WARNING: Be careful that your peptide info (begin,end) are correct.
getListSrnas() - Method in class bacnet.sequenceTools.SrnaView
getLocalization() - Method in class bacnet.datamodel.expdesign.BioCondition
getLocations() - Method in class org.biojava3.core.sequence.features.AbstractFeature: A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
getLocations() - Method in interface org.biojava3.core.sequence.features.FeatureInterface: The location(s) of this feature where the location should contain a reference to parent and sequence etc.
getLocusTag(String) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Look in all LocusTagToGeneName exists
getLocusTagCodingList(boolean) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Put in a list all the CodingSequence found
getLocusTagKnownCodingList(boolean) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
getLocusTagList(boolean) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Put in a list all the locusTag found in the list of genes
getLocusTagNonCodingList(boolean) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
getLocusTagToGeneNameMap() - Method in class bacnet.datamodel.sequence.Chromosome
getLocusTagToGeneNameMap() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getLocusTagToOldLocusTagMap() - Method in class bacnet.datamodel.sequence.Chromosome
getLOGFC_MATRIX_PROTEOMES_PATH() - Static method in class bacnet.Database: Path for loading Proteomes matrix data showing relative expression values
getLOGFC_MATRIX_TRANSCRIPTOMES_PATH() - Static method in class bacnet.Database: Path for loading Transcriptomes matrix data showing Log(Fold Change) values
getLogfcOmicsMatrix() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getLogFCProteomesTable(String) - Method in class bacnet.Database: Load Logfc proteome tables for a specific genome
getLogFCProteomeTable() - Method in class bacnet.Database
getLogFCTable() - Method in class bacnet.Database
getLogFCTranscriptomesTable(String) - Method in class bacnet.Database: Load logFC transcriptome table for a specific genome
getLogo() - Method in class bacnet.Database
getLogo(Sequence) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: For a given Sequence, return the nucleotide sequence before and after starting position
getLongName() - Method in class org.biojava3.core.sequence.compound.CodonCompound
getLongName() - Method in class org.biojava3.core.sequence.template.AbstractCompound
getLongName() - Method in interface org.biojava3.core.sequence.template.Compound
getLongName() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
getLongName() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getMappingFrame() - Method in class bacnet.datamodel.proteomics.NTerm
getMassSpecData() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getMatrices() - Method in class bacnet.datamodel.expdesign.BioCondition
getMatrices() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of SeqData given a bioCondName
getMatrices(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of SeqData given a bioCondName
getMatrix() - Method in class bacnet.datamodel.dataset.ExpressionData
getMatrix() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
getMatrix() - Method in class bacnet.table.core.Filter
getMatrix() - Method in class bacnet.table.core.FilterList
getMatrix() - Method in class bacnet.utils.Filter
getMatrixDisplayed() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
getMax() - Method in class bacnet.datamodel.dataset.ExpressionData
getMax() - Method in class bacnet.genomeBrowser.core.DataTrack
getMax() - Method in class bacnet.table.core.ColorMapper
getMax() - Method in class bacnet.table.core.ColorMapperRCP
getMax(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper: Scans through a list of locations to find the Location with the highest end
getMax(List<Location>) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools: Scans through a list of locations to find the Location with the highest end
getMaxColor() - Method in class bacnet.table.core.ColorMapper
getMaxColor() - Method in class bacnet.table.core.ColorMapperRCP
getMaxColorSWT() - Method in class bacnet.table.core.ColorMapper
getMaxColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getMaxPos() - Method in class bacnet.table.core.ColorMapper
getMaxPos() - Method in class bacnet.table.core.ColorMapperRCP
getMaxQuant() - Method in class bacnet.datamodel.proteomics.NTerm
getMaxQuantum() - Method in class bacnet.datamodel.proteomics.NTerm
getMaxSingleCompoundStringLength() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
getMaxSingleCompoundStringLength() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
getMaxSingleCompoundStringLength() - Method in interface org.biojava3.core.sequence.template.CompoundSet: Returns the maximum size of a compound String this set holds
getMean() - Method in class bacnet.datamodel.dataset.ExpressionData
getMean() - Method in class bacnet.table.core.ColorMapper
getMean() - Method in class bacnet.table.core.ColorMapperRCP
getMean(ArrayList<GeneExpression>, String) - Static method in class bacnet.datamodel.dataset.GeneExpression: Calculate the mean expression of list of Tiling
getMean(ArrayList<Tiling>, String) - Static method in class bacnet.datamodel.dataset.Tiling: Calculate the mean expression of list of Tiling
getMedia() - Method in class bacnet.datamodel.expdesign.BioCondition
getMediaGrowthProperties() - Method in class bacnet.datamodel.expdesign.BioCondition
getMedian() - Method in class bacnet.datamodel.dataset.ExpressionData
getMedian() - Method in class bacnet.table.core.ColorMapper
getMedian() - Method in class bacnet.table.core.ColorMapperRCP
getMedianValue(String) - Method in class bacnet.datamodel.dataset.GeneExpression: Get the median value of corresponding probe in double[][] values
getMedianVector() - Method in class bacnet.datamodel.dataset.GeneExpression: Extract the column containing the median
getMiddleH() - Method in class bacnet.genomeBrowser.core.Region
getMiddleV() - Method in class bacnet.genomeBrowser.core.Region
getMidLeftColor() - Method in class bacnet.table.core.ColorMapper
getMidLeftColor() - Method in class bacnet.table.core.ColorMapperRCP
getMidLeftColorSWT() - Method in class bacnet.table.core.ColorMapper
getMidLeftColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getMidLeftPos() - Method in class bacnet.table.core.ColorMapper
getMidLeftPos() - Method in class bacnet.table.core.ColorMapperRCP
getMidRightColor() - Method in class bacnet.table.core.ColorMapper
getMidRightColor() - Method in class bacnet.table.core.ColorMapperRCP
getMidRightColorSWT() - Method in class bacnet.table.core.ColorMapper
getMidRightColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getMidRightPos() - Method in class bacnet.table.core.ColorMapper
getMidRightPos() - Method in class bacnet.table.core.ColorMapperRCP
getMin() - Method in class bacnet.datamodel.dataset.ExpressionData
getMin() - Method in class bacnet.genomeBrowser.core.DataTrack
getMin() - Method in class bacnet.table.core.ColorMapper
getMin() - Method in class bacnet.table.core.ColorMapperRCP
getMin(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper: Scans through a list of locations to find the Location with the lowest start
getMin(List<Location>) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools: Scans through a list of locations to find the Location with the lowest start
getMinColor() - Method in class bacnet.table.core.ColorMapper
getMinColor() - Method in class bacnet.table.core.ColorMapperRCP
getMinColorSWT() - Method in class bacnet.table.core.ColorMapper
getMinColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getMinPos() - Method in class bacnet.table.core.ColorMapper
getMinPos() - Method in class bacnet.table.core.ColorMapperRCP
getMissingValuesFreeMatrix() - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Return a subMatrix containing only rows without Missingvalues
getModifications() - Method in class bacnet.datamodel.dataset.NTermData
getModifs() - Method in class bacnet.datamodel.proteomics.TIS
getModifSequence() - Method in class bacnet.datamodel.proteomics.NTerm
getModifsString() - Method in class bacnet.datamodel.proteomics.TIS
getMolecularWeight() - Method in class org.biojava3.core.sequence.compound.CodonCompound
getMolecularWeight() - Method in class org.biojava3.core.sequence.template.AbstractCompound
getMolecularWeight() - Method in interface org.biojava3.core.sequence.template.Compound
getMolecularWeight() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
getMolecularWeight() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getMolMass() - Method in class bacnet.datamodel.sequence.Gene
getMolMass(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getMouseXPosition() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getMouseXPosition() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getMouseYPosition() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getMouseYPosition() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getMraheilInfo() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the different tables from Mraheil et al. 2011 publication and create a list of sRNAs from the different tables
getMultiFasta() - Method in class bacnet.datamodel.sequence.Genome.GetMultiFastaThread
GetMultiFastaThread(HashMap<String, String>) - Constructor for class bacnet.datamodel.sequence.Genome.GetMultiFastaThread
getMULTIOMICS_MATRIX_PATH() - Static method in class bacnet.Database: Path for loading Proteomes matrix data showing relative expression values
getMULTIOMICS_PATH() - Static method in class bacnet.Database
getMutant() - Method in class bacnet.datamodel.expdesign.BioCondition
getName() - Method in class bacnet.datamodel.annotation.RfamElement
getName() - Method in class bacnet.datamodel.annotation.Signature
getName() - Method in class bacnet.datamodel.dataset.OmicsData
getName() - Method in class bacnet.datamodel.expdesign.BioCondition
getName() - Method in class bacnet.datamodel.expdesign.Experiment
getName() - Method in class bacnet.datamodel.sequence.Chromosome
getName() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getName() - Method in class bacnet.datamodel.sequence.Sequence
getName() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getName() - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
getName() - Method in class bacnet.table.core.Filter
getName() - Method in class bacnet.utils.Filter
getName() - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
getName(BlastOutput.BlastOutputTYPE) - Static method in class bacnet.scripts.blast.BlastOutput
getNameColumn() - Static method in class bacnet.datamodel.annotation.Annotation: Return the column index corresponding to Name
getNameMassSpecDataFinal() - Method in class bacnet.scripts.listeriomics.nterm.NTermCreateFinalData
getNameNTermData() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getNameRawData() - Method in class bacnet.datamodel.proteomics.NTermCreateData
getNavigationListener() - Method in class bacnet.Database
getNbElements() - Method in class bacnet.table.core.ColorMapper
getNbElements() - Method in class bacnet.table.core.ColorMapperRCP
getNbElementType() - Method in class bacnet.datamodel.annotation.Annotation
getNbSet() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
getNCBIGenomePhylogeny() - Static method in class bacnet.scripts.phylogeny.PhylogenyTools: From PhyloXMl of all bacteria, get only the genome which have a NCBI genome id
getNcRNAs() - Method in class bacnet.datamodel.sequence.Chromosome
getNcRNAs() - Method in class bacnet.datamodel.sequence.Genome: Return all NcRNAs in all chromosomes
getNCRNAUpstream(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: For each gene search if the end of a smallRNA or cisReg element is in the region -200bp - start codon
getNETWORK_PATH() - Static method in class bacnet.Database
getNewDocument() - Static method in class org.biojava3.core.util.XMLHelper
getNewLocusTag() - Method in class bacnet.datamodel.sequence.Gene
getNewRASTids() - Static method in class bacnet.scripts.genome.RASTEGDeGenome: Transform a list of old RAST ids into new RAST id
getNext() - Method in class bacnet.scripts.core.vennDiagram.CombinationGenerator
getNext() - Method in class bacnet.utils.CombinationGenerator
getNextCodon() - Method in class bacnet.datamodel.proteomics.NTerm
getNextNterm(NTerm, String) - Method in class bacnet.datamodel.dataset.NTermData: Given a NTerm, find the next one in the Annotation
getNGSSeqs() - Method in class bacnet.datamodel.expdesign.BioCondition
getNoDNAList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getNonCodingRegion(String) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence: Get the gene based on accession.
getNoncodingSequenceHashMap() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getNonCodingSequencesList(boolean) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Put in a list all the NonCodingSequence found
getNoProtList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getNoRNAList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getNotAssociatedList(String, boolean) - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Read list of gene not having been associated (RAST and NCBI association)
getNotDiffExpressedASrnas() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getNotDiffExpressedCisRegs() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getNotDiffExpressedGenes() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getNotDiffExpresseds() - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
getNotDiffExpressedSrnas() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getNote() - Method in class bacnet.datamodel.annotation.RfamElement
getNote() - Method in class bacnet.datamodel.dataset.OmicsData
getNote(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getNotesList() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getNotListeriaAndBacillusGenome() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Return a list of all NON Listeria genomes
getNotListeriaGenome() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Return a list of all NON Listeria genomes
getNTermDatas() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of NTermData given a bioCondName
getNTermDatas(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of NTermData given a bioCondName
getnTermExp() - Method in class bacnet.datamodel.proteomics.NTermFilter
getnTermHighlight() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getnTermRef() - Method in class bacnet.datamodel.proteomics.TIS
getnTerms() - Method in class bacnet.datamodel.expdesign.BioCondition
getnTerms() - Method in class bacnet.datamodel.proteomics.TIS
getNTerms() - Method in class bacnet.datamodel.dataset.NTermData: Return a list of all NTerms available
getnTermsSequences() - Method in class bacnet.datamodel.proteomics.TIS: Return a character string with all peptide Modif sequences
getnTermsString() - Method in class bacnet.datamodel.proteomics.TIS: Return a character string with all peptide names
getnTermTypeOverlap() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getNucleotideColor(String, Display) - Static method in class bacnet.datamodel.sequence.CompoundColorization: Given a Nucleotide, this method return the corresponding color
getNumberColumn() - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Get the number of column of the values array
getNumberColumnWithAnnotation() - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Get the number of column of the values array + annotations array
getNumberRow() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getNumericRepresentation() - Method in enum org.biojava3.core.sequence.Strand
getNumLeft() - Method in class bacnet.scripts.core.vennDiagram.CombinationGenerator
getNumLeft() - Method in class bacnet.utils.CombinationGenerator
getOldLocusTag() - Method in class bacnet.datamodel.sequence.Gene
getOldLocusTag(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getOliverInfo() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the different tables from Oliver et al. 2009 publication and create a list of sRNAs from the different tables
getOliverInfoEGDePosition() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the different tables from Oliver et al. 2009 publication and create a list of sRNAs from the different tables
getOmicsData() - Method in class bacnet.datamodel.expdesign.BioCondition: Put all OmicsData in a list
getOne() - Method in class org.biojava3.core.sequence.compound.CodonCompound
getOne() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
getOne() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getOperon() - Method in class bacnet.datamodel.sequence.Gene
getOperon(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getOperons() - Method in class bacnet.datamodel.sequence.Chromosome
getOperons() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getOperons() - Method in class bacnet.datamodel.sequence.Genome: Return all Operon in all chromosomes
getOrderedRowNames() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getOrganismName() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: Get the organism name assigned to this sequence
getOriginalHeader() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getOverASrnas() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getOverBioConds() - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
getOverCisRegs() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getOverExpressed() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getOverGenes() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getOverlap() - Method in class bacnet.datamodel.proteomics.NTerm
getOverlap(String, String, String) - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap
getOverlapingGene() - Method in class bacnet.datamodel.proteomics.TIS
getOverlapList(ArrayList<String>, String, String, String) - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Read NCBI and RAST genomes and look at overlapping elements
getOverlaps() - Method in class bacnet.datamodel.proteomics.TIS
getOverlapsString() - Method in class bacnet.datamodel.proteomics.TIS
getOverSrnas() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getParentChromosomeSequence() - Method in class org.biojava3.core.sequence.GeneSequence: The parent ChromosomeSequence which contains the actual DNA sequence data
getParentFeature() - Method in class org.biojava3.core.sequence.features.AbstractFeature: Get the parent Feature
getParentFeature() - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Get the parent feature
getParentGenome() - Method in class bacnet.datamodel.sequence.Chromosome
getParentGenome() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence: Get the gene based on accession.
getParentSequence() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getParentViewId() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getPartService() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getPath() - Method in class bacnet.Database
getPath(String) - Static method in class bacnet.utils.FileUtils: Get only the folder where the file is contained
getPATH() - Static method in class bacnet.datamodel.dataset.ExpressionData
getPATH() - Static method in class bacnet.datamodel.proteomics.NTermUtils
getPATH() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
getPDBCharacter(boolean, char, char, boolean, char) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Creates formatted String for a single character of PDB output
getPDBConservation(boolean, char, char, boolean) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Creates formatted String for displaying conservation in PDB output
getPDBLegend() - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Creates formatted String for displaying conservation legend in PDB output
getPeptides() - Method in class bacnet.datamodel.dataset.NTermData: Link peptideSequence to ArrayList(NTerm)
This correspond to the list of NTerm having same peptideSequence
getPhase() - Method in class org.biojava3.core.sequence.CDSSequence
getPhyloFigure(Gene, ArrayList<String>) - Static method in class bacnet.sequenceTools.GeneViewHomologTools: Read Phylogenomic figure and modify the labels with homolog table
getPhyloFigure(ArrayList<String>) - Method in class bacnet.sequenceTools.GenomicsView: DO NOT WORK WITH NEW VERSION OF FIGTREE Return the text file of the SVG figure, modified with highlighted strains
getPhylogenomicFigurePath() - Static method in class bacnet.datamodel.phylogeny.Phylogenomic: Test if the Phylogenomic figure exist and rturn its path
getPieChartData(HashMap<String, ArrayList<String>>) - Static method in class bacnet.datamodel.annotation.COGannotation: Transform the result of getCogClassification() method into an ExpressionMatrix which can be load by PieChartView for display
getPieChartData(HashMap<String, ArrayList<String>>) - Static method in class bacnet.datamodel.annotation.GlaserFCannotation: Transform the result of getGlaserFCclassification() method into an ExpressionMatrix which can be load by PieChartView for display
getPluginFileURL(String, String) - Static method in class bacnet.swt.ResourceManager: Returns an URL based on a Bundle and resource entry path.
getPluginImage(Object, String) - Static method in class bacnet.swt.ResourceManager: Deprecated.
Use ResourceManager.getPluginImage(String, String) instead.
getPluginImage(String, String) - Static method in class bacnet.swt.ResourceManager: Returns an Image based on a Bundle and resource entry path.
getPluginImageDescriptor(Object, String) - Static method in class bacnet.swt.ResourceManager: Deprecated.
Use ResourceManager.getPluginImageDescriptor(String, String) instead.
getPluginImageDescriptor(String, String) - Static method in class bacnet.swt.ResourceManager: Returns an ImageDescriptor based on a Bundle and resource entry path.
getPluginImageURL(Object, String) - Static method in class bacnet.swt.ResourceManager: Returns an URL based on a plugin and file path.
getPluginTextFile(String, String) - Static method in class bacnet.utils.HTMLUtils: Returns an String based on a Bundle and resource entry path.
getPosition() - Method in class org.biojava3.core.sequence.location.FuzzyPoint
getPosition() - Method in class org.biojava3.core.sequence.location.SimplePoint
getPosition() - Method in interface org.biojava3.core.sequence.location.template.Point: Returns the position held by this object
getPosition(int) - Method in class bacnet.datamodel.dataset.Tiling: Return the index position in the tiling matrix of a particular probes closest to bpPosition
getPreviousCodon() - Method in class bacnet.datamodel.proteomics.NTerm
getPreviousNterm(NTerm, String) - Method in class bacnet.datamodel.dataset.NTermData: Given a NTerm, find the previous one in the Annotation
getPrideLink(String) - Static method in class bacnet.utils.RWTUtils: Get pride database link to a specific project
getProbes() - Method in class bacnet.datamodel.dataset.GeneExpression
getProbes() - Method in class bacnet.datamodel.dataset.Tiling
getProbesGExpression() - Method in class bacnet.Database: Read probes for GExpression in GeneExpression.PROBES_PATH
getProbesTiling() - Method in class bacnet.Database: Read probes for Tiling in Tiling.PROBES_PATH
getProduct() - Method in class bacnet.datamodel.sequence.Gene
getProduct() - Method in class bacnet.datamodel.sequence.NcRNA
getProduct(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getProjectName() - Method in class bacnet.Database
getProperties() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo: Get the properties
getProtein_id() - Method in class bacnet.datamodel.sequence.Gene
getProteinCDSSequences() - Method in class org.biojava3.core.sequence.TranscriptSequence: Return a list of protein sequences based on each CDS sequence where the phase shift between two CDS sequences is assigned to the CDS sequence that starts the triplet.
getProteinID(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Search for protein-id in the Note section of Gene
Search first : protein_id attribute
Search then : protein_Id attribute
Finally in CDS section of Note search for: "Dbxref :" and "Genbank:" protein id
getProteinIDTolocusTag() - Method in class bacnet.datamodel.sequence.Chromosome
getProteinIDToOldLocusTagMap() - Method in class bacnet.datamodel.sequence.Chromosome
getProteinNCBILink(String) - Static method in class bacnet.utils.RWTUtils
getProteinSequence() - Method in class org.biojava3.core.sequence.RNASequence: Get the ProteinSequence from the RNA sequence
getProteinSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence: Get the protein sequence
getProteinSequence(TranscriptionEngine) - Method in class org.biojava3.core.sequence.RNASequence: Get the ProteinSequene from the RNA sequence with user defined transcription engine
getProteinSequence(TranscriptionEngine) - Method in class org.biojava3.core.sequence.TranscriptSequence: Get the protein sequence with user defined TranscriptEngine
getProteinSequenceCreator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getProteinSequenceFromFasta(String, String) - Static method in class bacnet.datamodel.sequence.Genome: Read all accessible FAA files to extract protein sequence of a gene
getProteinSequences() - Method in class org.biojava3.genome.parsers.geneid.GeneIDXMLReader
getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava3.genome.GeneFeatureHelper
getProteolyseAssociated(NTerm) - Method in class bacnet.datamodel.dataset.NTermData: Go through proteolyses map, and find the list of NTerm which might be associated to an input NTerm
Warning: ArrayList in return contains key NTerm of proteolyses but not the input nTerm
getProteomeGenomes() - Static method in class bacnet.datamodel.expdesign.BioCondition: Get all genomes associated to a proteomics dataset
getProteomes() - Method in class bacnet.datamodel.expdesign.BioCondition
getProteomes() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of MassSpecData given a bioCondName
getProteomes() - Method in class bacnet.scripts.database.DataValidation
getProteomes(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of MassSpecData given a bioCondName
getPROTEOMES_PATH() - Static method in class bacnet.Database
getProteomesArrayPath() - Method in class bacnet.Database
getProteomesComparisonsArrayPath() - Method in class bacnet.Database
getProteomicsData() - Method in class bacnet.datamodel.expdesign.BioCondition: Put all OmicsData in a list
getProxySequenceReader() - Method in interface org.biojava3.core.sequence.location.template.AccesionedLocation: Return the proxy reader used to get sequence for this location.
getProxySequenceReader() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getPubMedLink(String) - Static method in class bacnet.utils.RWTUtils
getQualities() - Method in class org.biojava3.core.sequence.features.QualityFeature
getQualities(int, int) - Method in class org.biojava3.core.sequence.features.QualityFeature
getQualityAt(int) - Method in class org.biojava3.core.sequence.features.QualityFeature
getQuantities() - Method in class org.biojava3.core.sequence.features.QuantityFeature
getRASTinfo() - Method in class bacnet.datamodel.sequence.Gene
getRASTinfo(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getRawDatas() - Method in class bacnet.datamodel.dataset.OmicsData
getRead() - Method in class bacnet.datamodel.dataset.ExpressionData
getRed() - Method in class bacnet.table.core.ColorSWT
getRef() - Method in class bacnet.datamodel.sequence.Sequence
getReference() - Method in class bacnet.datamodel.annotation.Signature
getReference() - Method in class bacnet.datamodel.expdesign.BioCondition
getRefSequence() - Method in class bacnet.datamodel.proteomics.TIS
getRegulatoryRegion() - Static method in class bacnet.scripts.listeriomics.nterm.NTermTranscriptome
getRelevantSubLocations() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation: Returns the normalised list of sub locations i.e. only those locations which do not have a sub location.
getRelevantSubLocations() - Method in interface org.biojava3.core.sequence.location.template.Location: An extension to Location.getSubLocations() which returns sub-locations of sub-locations; this will continue until it runs out of those locations.
getRelevantSubSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
getRelevantSubSequence(Sequence<C>) - Method in interface org.biojava3.core.sequence.location.template.Location: Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented
getResultsFromXML(String) - Static method in class bacnet.scripts.blast.BlastResult: From an XML blast file, extract blast results
getReverse() - Method in class org.biojava3.core.sequence.DNASequence: Returns a Sequence which runs in the current reverse order
getReverse() - Method in enum org.biojava3.core.sequence.Strand
getReverseComplement() - Method in class org.biojava3.core.sequence.DNASequence: Delegates to AbstractSequence.getInverse() for the reverse complement
getReverseComplement() - Method in class org.biojava3.core.sequence.RNASequence: Get reverse complement view of the sequence
getReverseFrames() - Static method in enum org.biojava3.core.sequence.transcription.Frame: Returns all frames which are in the reverse orientation
getRfamDirectory() - Static method in class bacnet.datamodel.annotation.RfamElement: Project.getANNOTATION_PATH()+"RfamData"+File.separator;
getRfamElementsFromGenome(String) - Static method in class bacnet.datamodel.annotation.RfamElement: Return the list of Rfam element in a particular Genome

Search for all NCBI GFF in a particular genome folder (e.g. genomeName),
thanks to RFAM_GENOME table it found corresponding Rfam GFF file if it exists
and create HashMap<String, RfamElement> rfamList
getRfamElementsFromGFF(String) - Static method in class bacnet.datamodel.annotation.RfamElement: Read a Gff from Rfam and get all possible information
getRfamElementsFromGFF(String, HashMap<String, RfamElement>) - Static method in class bacnet.datamodel.annotation.RfamElement: Read a Gff from Rfam and add the information to an existing HashMap
getRfamGenomeId(String) - Static method in class bacnet.datamodel.annotation.RfamElement: Given an NCBI Gff file name, this function search in RFAM_GENOME table and return Rfam Gff file name if it exists
getRfamID() - Method in class bacnet.datamodel.sequence.Srna
getRfamInfo() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the different tables from Rfam 2011 data and create a list of sRNAs from the different tables
getRiboSeqDatas() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of SeqDatas
getRiboSeqDatas(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of RiboSeqData given a bioCondName
getRightBCs() - Method in class bacnet.scripts.core.Comparison
getRnaAminoAcidTranslator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getRnaCompounds() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getRNACompoundSet() - Static method in class org.biojava3.core.sequence.compound.RNACompoundSet
getRNASeqDatas() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of SeqDatas
getRNASeqDatas(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of RNASeqData given a bioCondName
getRNASeqGenomes() - Static method in class bacnet.datamodel.expdesign.BioCondition: Get all genomes associated to a transcriptomes dataset
getRNASeqs() - Method in class bacnet.datamodel.expdesign.Experiment: Return all NGS data contains in all BioCondition
getRNASequence() - Method in class org.biojava3.core.sequence.DNASequence: Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
getRNASequence(Frame) - Method in class org.biojava3.core.sequence.DNASequence: Allows the user to pass in the Frame shift.
getRNASequence(TranscriptionEngine) - Method in class org.biojava3.core.sequence.DNASequence: Allow a user to pass in a rules engine to do the DNA to RNA translation
getRNASequence(TranscriptionEngine, Frame) - Method in class org.biojava3.core.sequence.DNASequence
getRnaSequenceCreator() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getRnaToDna() - Method in class org.biojava3.core.sequence.views.RnaSequenceView
getRow(double[][], int) - Static method in class bacnet.utils.ArrayUtils
getRow(int[][], int) - Static method in class bacnet.utils.ArrayUtils
getRow(String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getRow(String[][], int) - Static method in class bacnet.utils.ArrayUtils: Extract a Row from a Matrix
getRowName(int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getRowNameCellColor() - Method in class bacnet.table.core.ColorMapper
getRowNames() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getRowNamesToList() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getRowNameTextColor() - Method in class bacnet.table.core.ColorMapper
getRscriptDirectory() - Static method in class bacnet.scripts.core.Rscript: Test if the R script directory has been given, and open a dialog to update it in case
getSameEndList(String, boolean) - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Read list of gene having same end position but different starting point
getScore() - Method in class bacnet.datamodel.annotation.RfamElement
getScore() - Method in class bacnet.datamodel.proteomics.NTerm
getScrolledComposite() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getScrolledComposite() - Method in class bacnet.sequenceTools.SrnaView
getSDEnergy(Gene) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: Return the binding energy with aSD sequence
getSDRFCuratedPath(String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Get path of curated SDRF file for a specific dataID (ex: E-MTAB-1800)
getSDRFCuratedPath(String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Get path of curated SDRF file for a specific dataID (ex: E-MTAB-1800)
getSDRFPath(String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Get path of SDRF file for a specific dataID (ex: E-MTAB-1800)
getSDRFPath(String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Get path of SDRF file for a specific dataID (ex: E-MTAB-1800)
getSDSequence() - Method in class bacnet.datamodel.sequence.Sequence: Get the nucleotide sequence 20bp upstream to the Sequence, +3bp for including start codon
getSDSequence(int) - Method in class bacnet.datamodel.sequence.Sequence: Get the nucleotide sequence n bp upstream to the Sequence, +3bp for including start codon
getSecondRowName() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getSelectedComparisons() - Method in class bacnet.sequenceTools.GeneView: Return the list of comparisons which have been selected
getSelectedComparisons() - Method in class bacnet.sequenceTools.SrnaView: Return the list of comparisons which have been selected
getSelectedComparisonsProteome() - Method in class bacnet.sequenceTools.GeneView
getSelectedGenes() - Method in class bacnet.sequenceTools.AnnotationView
getSeq() - Method in class bacnet.sequenceTools.SrnaView
getSeqDatas(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of RNASeqData given a bioCondName
getSeqeunceFromString(String) - Method in class org.biojava3.core.util.SequenceTools
getSequence() - Method in class bacnet.datamodel.sequence.Sequence: Read chromosome and extract the corresponding sequence as a String
getSequence() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getSequence() - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
getSequence() - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
getSequence() - Method in class bacnet.sequenceTools.GeneView
getSequence() - Method in class org.biojava3.core.sequence.location.SequenceLocation
getSequence(DataInput, int) - Method in class org.biojava3.core.sequence.io.FastaSequenceParser
getSequence(DataInput, int) - Method in interface org.biojava3.core.sequence.io.template.SequenceParserInterface
getSequence(String) - Method in class bacnet.datamodel.sequence.Chromosome: Given a sequence name, return the corresponding Sequence
If name is a Gene name, we search also in geneNameToLocusTagMap
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.DNASequenceCreator
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator: Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator: Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.ProteinSequenceCreator
getSequence(String, long) - Method in class org.biojava3.core.sequence.io.RNASequenceCreator
getSequence(String, long) - Method in interface org.biojava3.core.sequence.io.template.SequenceCreatorInterface
getSequence(List<C>) - Method in interface org.biojava3.core.sequence.io.template.SequenceCreatorInterface
getSequence(List<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator: Assumes all compounds were uppercase
getSequence(List<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator: Not sure of use case and currently not supported
getSequence(List<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.io.ProteinSequenceCreator
getSequence(List<NucleotideCompound>) - Method in class org.biojava3.core.sequence.io.DNASequenceCreator
getSequence(List<NucleotideCompound>) - Method in class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator: Not sure of use case and currently not supported
getSequence(List<NucleotideCompound>) - Method in class org.biojava3.core.sequence.io.RNASequenceCreator
getSequence(ProxySequenceReader<C>, long) - Method in interface org.biojava3.core.sequence.io.template.SequenceCreatorInterface
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava3.core.sequence.io.FileProxyProteinSequenceCreator: Should be able to extend the same concept to a remote URL call or database connection.
getSequence(ProxySequenceReader<AminoAcidCompound>, long) - Method in class org.biojava3.core.sequence.io.ProteinSequenceCreator
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava3.core.sequence.io.DNASequenceCreator
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava3.core.sequence.io.FileProxyDNASequenceCreator: Should be able to extend the same concept to a remote URL call or database connection.
getSequence(ProxySequenceReader<NucleotideCompound>, long) - Method in class org.biojava3.core.sequence.io.RNASequenceCreator
getSequence5PrimeTo3Prime() - Method in class org.biojava3.core.sequence.GeneSequence: Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand
getSequenceAA() - Method in class bacnet.datamodel.sequence.Sequence: Get Amino Acid sequence of a Sequence
getSequenceAACurated() - Method in class bacnet.datamodel.sequence.Sequence: When an Amino Acid sequence contains Stop codon ('*'), this method search the first start codon and remove sequence before, and then create different sequence, from one stop codon to the other.
getSequenceAACurated(String) - Static method in class bacnet.datamodel.sequence.Sequence: When an Amino Acid sequence contains Stop codon ('*'), this method search the first start codon and remove sequence before, and then create different sequence, from one stop codon to the other.
getSequenceAsString() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getSequenceAsString() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getSequenceAsString() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns the sequence as a String
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getSequenceAsString() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Delegates to SequenceMixin.toList(org.biojava3.core.sequence.template.Sequence)
getSequenceAsString() - Method in class org.biojava3.core.sequence.template.AbstractSequence: Default case is to assume strand is positive because only CDSSequence can be either positive or negative Strand.
getSequenceAsString() - Method in interface org.biojava3.core.sequence.template.Sequence: Returns the String representation of the Sequence
getSequenceAsString() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getSequenceAsString() - Method in class org.biojava3.core.sequence.views.ComplementSequenceView
getSequenceAsString() - Method in class org.biojava3.core.sequence.views.ReversedSequenceView
getSequenceAsString() - Method in class org.biojava3.core.sequence.views.RnaSequenceView
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getSequenceAsString(Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.template.AbstractSequence
getSequenceAsString(List<C>, CompoundSet<C>, Integer, Integer, Strand) - Method in class org.biojava3.core.sequence.storage.SequenceAsStringHelper
getSequenceCollection() - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
getSequenceMap() - Method in class bacnet.datamodel.proteomics.NTerm
getSequencePeptide() - Method in class bacnet.datamodel.proteomics.NTerm
getSequenceRNA() - Method in class bacnet.datamodel.sequence.Sequence: Return RNA sequence of the Sequence
getSequenceScore() - Method in class org.biojava3.core.sequence.template.AbstractSequence: Provide place holder for a metric that indicate a score associated with the sequence
getSequenceUsage() - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
getSerialversionuid() - Static method in class bacnet.datamodel.annotation.Annotation
getSerialversionuid() - Static method in class bacnet.datamodel.dataset.ExpressionData
getSerialversionuid() - Static method in class bacnet.datamodel.dataset.NTermData
getSerialversionuid() - Static method in class bacnet.datamodel.dataset.OmicsData
getSerialversionuid() - Static method in class bacnet.datamodel.expdesign.Experiment
getSerialversionuid() - Static method in class bacnet.datamodel.proteomics.NTerm
getSerialversionuid() - Static method in class bacnet.datamodel.sequence.Gene
getSerialversionuid() - Static method in class bacnet.datamodel.sequence.NcRNA
getSerialversionuid() - Static method in class bacnet.datamodel.sequence.Sequence
getSerialversionuid() - Static method in class bacnet.datamodel.sequence.Srna
getSerialversionuid() - Static method in class bacnet.genomeBrowser.core.Track
getSerialversionuid() - Static method in class bacnet.table.core.ColorMapper
getSetNames() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
getSets() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
getShell() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getShortDescription() - Method in class org.biojava3.core.sequence.features.AbstractFeature
getShortDescription() - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Get the short description that can be used to describe the feature
getShortName() - Method in class org.biojava3.core.sequence.compound.CodonCompound
getShortName() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
getShortName() - Method in class org.biojava3.core.sequence.template.AbstractCompound
getShortName() - Method in interface org.biojava3.core.sequence.template.Compound
getShortName() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
getShortName() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getShowInfo() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getSignature() - Method in class bacnet.expressionAtlas.core.SignatureSelectionDialog
getSignatureFromName(String) - Static method in class bacnet.datamodel.annotation.Signature: Load serialized signature
getSignatures() - Method in class bacnet.datamodel.sequence.Sequence
getSIGNATURES_PATH() - Static method in class bacnet.Database
getSignaturesFromTextFiles() - Static method in class bacnet.datamodel.annotation.Signature: Read all signatures in txt format from the folder Database.getSIGNATURES()
getSignaturesNametoID() - Method in class bacnet.Database
getSignaturesToString() - Method in class bacnet.datamodel.sequence.Sequence
getSize() - Method in class bacnet.datamodel.annotation.Signature
getSize() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Get the number of sequences in the MSA
getSize() - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns the number of rows in this profile.
getSliderHbar() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getSliderVBar() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getSource() - Method in class org.biojava3.core.sequence.features.AbstractFeature: The feature source
getSource() - Method in interface org.biojava3.core.sequence.features.FeatureInterface: The source of the feature.
getSource() - Method in class org.biojava3.core.sequence.template.AbstractSequence: Added support for the source of this sequence for GFF3 export If a sub sequence doesn't have source then check for parent source
getSpecies() - Method in class bacnet.Database
getSpecies() - Method in class bacnet.datamodel.annotation.RfamElement
getSpecies() - Method in class bacnet.datamodel.sequence.Genome
getSpecies() - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
getSpectra() - Method in class bacnet.datamodel.proteomics.NTerm
getSpectrum() - Method in class bacnet.datamodel.proteomics.NTerm
getsRNAListEGDe() - Method in class bacnet.Database
getSrnaOrder() - Static method in class bacnet.datamodel.sequence.Srna: Return an ArrayList containing Srna names in the proper order
The list is load from PATH_LISTSRNA
getsRNAs() - Method in class bacnet.datamodel.sequence.Chromosome
getsRNAs() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
getsRNAs() - Method in class bacnet.datamodel.sequence.Genome: Return all Srnas in all chromosomes
getStart() - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit
getStart() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
getStart() - Method in interface org.biojava3.core.sequence.location.template.Location: Start of the location
getStartCode() - Method in class bacnet.datamodel.proteomics.NTerm
getStartCodon() - Method in class bacnet.datamodel.proteomics.NTerm
getStartCodon(Gene) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: Return start codon proportion in the genome
getStartCodonBefore() - Static method in class bacnet.datamodel.proteomics.NTermUtils: NOT FINISHED

Search for the different start codon before a peptide, and the stop codon after this peptide
Print the nucleotide sequence plus the codon, and identify Start, STOp and the reference Peptide used
getStartCodonSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence
getStat() - Method in class bacnet.datamodel.dataset.NTermData: Sysout some statistics about the number of aTIS, dTISM, dTIS, and uTIS
getSTAT_MATRIX_PROTEOMES_PATH() - Static method in class bacnet.Database: Path for loading Proteomes matrix data showing Fold Change values
getSTAT_MATRIX_TRANSCRIPTOMES_PATH() - Static method in class bacnet.Database: Path for loading Transcriptomes matrix data showing statistical p-values
getStatTable() - Method in class bacnet.Database
getStopCodonSequence() - Method in class org.biojava3.core.sequence.TranscriptSequence
getStrand() - Method in class bacnet.datamodel.annotation.RfamElement
getStrand() - Method in class bacnet.datamodel.sequence.Sequence
getStrand() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
getStrand() - Method in class org.biojava3.core.sequence.CDSSequence
getStrand() - Method in class org.biojava3.core.sequence.GeneSequence: A gene should have Strand
getStrand() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
getStrand() - Method in interface org.biojava3.core.sequence.location.template.Location: Strand which the location is located on
getStrand() - Method in class org.biojava3.core.sequence.TranscriptSequence
getStrand(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getStrandHeaders(boolean) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Return a list of the data contain in this matrix which correspond to a given strand
getStringForCompound(C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
getStringForCompound(C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
getStringForCompound(AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
getStringRepresentation() - Method in enum org.biojava3.core.sequence.Strand
getStudyName() - Method in class bacnet.datamodel.expdesign.BioCondition
getSubCodingSequencesList(ArrayList<String>, boolean) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Put in a sublist all the CodingSequence found in locuTag list
getSubLocations() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
getSubLocations() - Method in interface org.biojava3.core.sequence.location.template.Location: Gives access to the sub locations for this location.
getSubMatrix(ArrayList<String>, ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getSubMatrixColumn(ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Extract a matrix with only selected columns
getSubMatrixRow(ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Provide a list of rowName and extract them from the ExpressionMatrix
getSubMatrixRow(TreeSet<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Provide a list of rowName and extract them from the ExpressionMatrix
getSubMatrixRowRandom(double) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Generate a subMatrix with random rows
getSubRow(String, ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getSubSequence(int, int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Returns a sub sequence view
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Creates a SequenceProxyView for the given coordinates
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.template.AbstractSequence
getSubSequence(Integer, Integer) - Method in interface org.biojava3.core.sequence.template.Sequence: Returns a portion of the sequence from the different positions.
getSubSequence(Integer, Integer) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getSubSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.location.template.AbstractLocation: If circular this will return the sequence represented by the sub locations joined.
getSubSequence(Sequence<C>) - Method in interface org.biojava3.core.sequence.location.template.Location: Will return a SequenceReader object which represents the outer bounds of this Location
getSubsetNames() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
getSubsets() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
getSummaryTables(NTermData, String) - Static method in class bacnet.datamodel.proteomics.NTermSummaryTable
getSynonym() - Method in class bacnet.datamodel.sequence.Sequence
getSynonymsText() - Method in class bacnet.datamodel.sequence.Sequence
getTabFolder() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getTabFolder() - Method in class bacnet.sequenceTools.GeneView
getTabFolder() - Method in class bacnet.sequenceTools.SrnaView
getTabFolder() - Method in class bacnet.views.CoExprNetworkView
getTable() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getTable() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine
getTable(Integer) - Method in class org.biojava3.core.sequence.io.IUPACParser: Returns a table by its identifier i.e. 1 means universal codon tables
getTable(String) - Method in class org.biojava3.core.sequence.io.IUPACParser: Returns a table by its name
getTableBioCondition() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getTableBioCondition() - Method in class bacnet.genomeBrowser.NTerminomicsView
getTableBioCondition() - Method in class bacnet.sequenceTools.AnnotationView
getTableComposite() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getTableComposite() - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
getTableComposite() - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
getTableComposite() - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
getTableComposite() - Method in class bacnet.table.TableSWTView
getTableElementName() - Method in class bacnet.table.core.Filter
getTableElementName() - Method in class bacnet.utils.Filter
getTableGenes() - Method in class bacnet.sequenceTools.GeneView
getTableGenes() - Method in class bacnet.views.CoExprNetworkView
getTableNodiff() - Method in class bacnet.sequenceTools.GeneView
getTableNodiffProteome() - Method in class bacnet.sequenceTools.GeneView
getTableOtherInfo() - Method in class bacnet.sequenceTools.SrnaView
getTableOver() - Method in class bacnet.sequenceTools.GeneView
getTableOverProteome() - Method in class bacnet.sequenceTools.GeneView
getTableProteomes() - Method in class bacnet.sequenceTools.GeneView
getTables() - Method in class org.biojava3.core.sequence.io.IUPACParser: Returns a list of all available IUPAC tables
getTableSDRF(String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils: Return table found in DATA_TABLE
getTableSDRF(String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils: Return table found in DATA_TABLE
getTableSrnas() - Method in class bacnet.sequenceTools.SrnaView
getTableTranscriptomes() - Method in class bacnet.sequenceTools.GeneView
getTableUnder() - Method in class bacnet.sequenceTools.GeneView
getTableUnderProteome() - Method in class bacnet.sequenceTools.GeneView
getTargetSequence(Sequence<C>) - Method in class org.biojava3.core.sequence.edits.Edit.AbstractEdit: Returns the Sequence which is our edit.
getTaxonomy() - Method in class org.biojava3.core.sequence.template.AbstractSequence
getTbtmGraphVisualization() - Method in class bacnet.views.CoExprNetworkView
getTbtmHeatmap() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getTbtmScatterPlot() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getTechnoName(String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressTechnology: Given an ArrayDesgin ID return the full name of the microarray
getTechnoName(String) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology: Given an ArrayDesgin ID return the full name of the microarray
getTEMP_PATH() - Static method in class bacnet.Database
getTemperature() - Method in class bacnet.datamodel.expdesign.BioCondition
getTermSeqDatas() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of SeqDatas
getTermSeqDatas(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of Term given a bioCondName
getTests() - Method in class bacnet.scripts.core.Comparison
getText() - Method in class bacnet.raprcp.DownloadServiceHandler
getTextColor() - Method in class bacnet.table.core.ColorMapper
getTextColor() - Method in class bacnet.table.core.ColorMapperRCP
getTextColorSWT() - Method in class bacnet.table.core.ColorMapper
getTextColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getTextCutOff() - Method in class bacnet.views.CoExprNetworkView
getTextHeaderColor() - Method in class bacnet.table.core.ColorMapperRCP
getTextHeaderColorSWT() - Method in class bacnet.table.core.ColorMapper
getTextHeaderColorSWT() - Method in class bacnet.table.core.ColorMapperRCP
getTextSearch() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
getTextSearch() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
getThreadPool() - Static method in class org.biojava3.core.util.ConcurrencyTools: Returns current shared thread pool.
getThree() - Method in class org.biojava3.core.sequence.compound.CodonCompound
getThree() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
getThree() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getThreshold() - Method in class bacnet.datamodel.proteomics.NTerm
getTilingData(ArrayList<String>) - Static method in class bacnet.datamodel.dataset.Tiling: List all TilingData available by biocondName.
getTilingData(ArrayList<String>, ArrayList<String>) - Static method in class bacnet.datamodel.dataset.Tiling: Load all Tiling present in leftBCs and rightBCs.
getTilings() - Static method in class bacnet.datamodel.dataset.EGDeWTdata: Read all Tiling data corresponding to NAME_Mean, and return an ArrayList of Tiling
getTilings() - Method in class bacnet.datamodel.expdesign.BioCondition
getTilings() - Method in class bacnet.datamodel.expdesign.Experiment: Return all Tiling data contains in all BioCondition
getTilings() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of Tilings
getTilings(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of Tiling given a bioCondName
getTime() - Method in class bacnet.datamodel.expdesign.BioCondition
getTIRStructureEnergy(Gene) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: For very gene read TIRStructure.excel and extract the mean value of energy: We calculate the 2nd structure free energy and save it a table
And we calculate the energy for 40 different sequence: -20+40 to -20+80 and calculate the average energy
getTisList() - Method in class bacnet.datamodel.dataset.NTermData
getTisMap() - Method in class bacnet.datamodel.dataset.NTermData
getTISName() - Method in class bacnet.datamodel.proteomics.NTerm
getTIStoDisplay(ArrayList<NTerm>) - Method in class bacnet.datamodel.dataset.NTermData: Return the list of from a List of NTerm
getTitleFont() - Static method in class bacnet.swt.SWTResourceManager: Get the TITLE Font with appropriate height and style
getTitleFont(int) - Static method in class bacnet.swt.SWTResourceManager: Get the TITLE Font with appropriate height and style
getToCompoundSet() - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
getToledoInfo() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the different tables from Toledo-Arana publication and create a list of sRNAs from the different tables
getToolBar() - Method in class bacnet.e4.rap.BannerView
getTotal() - Method in class bacnet.scripts.core.vennDiagram.CombinationGenerator
getTotal() - Method in class bacnet.utils.CombinationGenerator
getTotalBP() - Method in class bacnet.genomeBrowser.core.Zoom
getTotalColumnSize(ArrayList<ExpressionMatrix>) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix: Return the number of column of the first ExpressionMatrix
getTotalRowSize(ArrayList<ExpressionMatrix>) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix: Count the total Number of row if we concatenate all ExpressionMatrix in the ArrayList
getTotalSpectra() - Method in class bacnet.datamodel.proteomics.TIS
getTotalSpectrum(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: For each gene add the number of spectra of every peptide available (not only aTIS peptides)
getTrack() - Method in class bacnet.genomeBrowser.core.DataTrack
getTrack() - Method in class bacnet.genomeBrowser.dialog.AddProteomicsDataDialog
getTrack() - Method in class bacnet.genomeBrowser.dialog.AddTranscriptomicsDataDialog
getTrack() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
getTrack() - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
getTrack() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getTrack() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getTrack() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
getTrackComposite() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getTrackGenome() - Method in class bacnet.sequenceTools.GeneView
getTracksComposite() - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
getTranscript(String) - Method in class org.biojava3.core.sequence.GeneSequence: Get the transcript sequence by accession
getTranscriptomes() - Method in class bacnet.scripts.database.DataValidation
getTranscriptomes() - Static method in class bacnet.scripts.listeriomics.nterm.NTermTranscriptome
getTRANSCRIPTOMES_PATH() - Static method in class bacnet.Database
getTranscriptomesArrayPath() - Method in class bacnet.Database
getTranscriptomesComparisonsArrayPath() - Method in class bacnet.Database
getTranscriptomesData() - Method in class bacnet.datamodel.expdesign.BioCondition: Put all TranscriptomeData in a list
getTranscriptomesGenomes() - Static method in class bacnet.datamodel.expdesign.BioCondition: Get all genomes associated to a transcriptomes dataset
getTranscripts() - Method in class org.biojava3.core.sequence.GeneSequence: Get the collection of transcription sequences assigned to this gene
getTranstable(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getTriplet() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getTriplicateValue(String) - Method in class bacnet.datamodel.dataset.GeneExpression: Get all technical replicates values of corresponding probe in double[][] values
getTSSDatas() - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of SeqDatas
getTSSDatas(String) - Method in class bacnet.genomeBrowser.core.DataTrack: Return the list of TSS given a bioCondName
getTssDownCoverage() - Method in class bacnet.datamodel.proteomics.NTerm
getTssDownDistance() - Method in class bacnet.datamodel.proteomics.NTerm
getTssDowntype() - Method in class bacnet.datamodel.proteomics.NTerm
getTssUpCoverage() - Method in class bacnet.datamodel.proteomics.NTerm
getTssUpDistance() - Method in class bacnet.datamodel.proteomics.NTerm
getTssUptype() - Method in class bacnet.datamodel.proteomics.NTerm
getTwo() - Method in class org.biojava3.core.sequence.compound.CodonCompound
getTwo() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
getTwo() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
getTxtCutoffLogFC() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getTxtCutoffLogFC() - Method in class bacnet.sequenceTools.GeneView
getTxtCutoffLogFCProteome() - Method in class bacnet.sequenceTools.GeneView
getTxtCutoffPvalue() - Method in class bacnet.sequenceTools.GeneView
getTxtSearch() - Method in class bacnet.genomeBrowser.NTerminomicsView
getTxtSearch() - Method in class bacnet.sequenceTools.AnnotationView
getTxtSearch() - Method in class bacnet.sequenceTools.GenomicsView
getTxtSeqnucleotide() - Method in class bacnet.sequenceTools.SrnaView
getType() - Method in class bacnet.datamodel.annotation.RfamElement
getType() - Method in class bacnet.datamodel.annotation.Signature
getType() - Method in class bacnet.datamodel.dataset.OmicsData
getType() - Method in class bacnet.datamodel.sequence.Sequence
getType() - Method in class bacnet.scripts.core.stat.StatTest
getType() - Method in class bacnet.table.core.ColorMapper: GETTERS and SETTERS
getType() - Method in class bacnet.table.core.ColorMapperRCP: GETTERS and SETTERS
getType() - Method in class org.biojava3.core.sequence.features.AbstractFeature: The feature type
getType() - Method in interface org.biojava3.core.sequence.features.FeatureInterface: The type of the feature.
getType(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
getTypeColumn() - Static method in class bacnet.datamodel.annotation.Annotation: Return the column index corresponding to Type
getTypeData() - Method in class bacnet.scripts.core.Expression
getTypeDataContained() - Method in class bacnet.datamodel.expdesign.BioCondition
getTypeFilter() - Method in class bacnet.table.core.Filter
getTypeFilter() - Method in class bacnet.utils.Filter
getTypeModif() - Method in class bacnet.datamodel.proteomics.NTerm
getTypeNcRNA() - Method in class bacnet.datamodel.sequence.NcRNA
getTypeOfTIS(String) - Method in class bacnet.datamodel.dataset.NTermData: Return a HashMap of NTerm with nTerm.getTypeOverlap() == typeOverlap
getTypeOverlap() - Method in class bacnet.datamodel.proteomics.NTerm
getTypeOverlaps() - Method in class bacnet.datamodel.dataset.NTermData
getTypeOverlaps() - Method in class bacnet.datamodel.proteomics.NTermFilter
getTypeSrna() - Method in class bacnet.datamodel.sequence.Srna
getUnderASrnas() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getUnderBioConds() - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
getUnderCisRegs() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getUnderExpressed() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getUnderGenes() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getUnderlyingCompound() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
getUnderSrnas() - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
getUniprotbaseURL() - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: The current unirpot URL to deal with caching issues. www.uniprot.org is loaded balanced but you can access pir.uniprot.org directly.
getUniprotDirectoryCache() - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: Local directory cache of XML that can be downloaded
getUnknownRAST(String, String) - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap: Read the list of RAST elements totally unknown and create a list of Sequence from it
getUnlogValue(int, String) - Method in class bacnet.datamodel.dataset.NGS: Get value at a certain base pair position and unlog it by calculating 2^value
It works faster if data has been already loaded by this.read() or this.read(from,to)
getUpDNAList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getUpperedBase() - Method in class org.biojava3.core.sequence.template.AbstractCompound
getUpProtList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getUpRNAList() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getURL() - Static method in class bacnet.raprcp.NavigationManagement: Return the current URL of your RAP project
getUserCollection() - Method in class org.biojava3.core.sequence.template.AbstractSequence: Provided for convience if the developer needs to associate data with a sequence
getUserObject() - Method in class org.biojava3.core.sequence.features.AbstractFeature
getUserObject() - Method in interface org.biojava3.core.sequence.features.FeatureInterface
getUTRLength() - Method in class bacnet.datamodel.proteomics.TIS
getUTRLength(Gene) - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: Deprecated.
getValue() - Method in class org.biojava3.core.util.CRC64Checksum
getValue(int) - Method in class bacnet.datamodel.dataset.ExpressionData: Return the value at the right position in the double[] values argument
Read the data if necessary
getValue(int, int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getValue(String, String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Get value in the ExpressionMatrix
getValueAnnotation(int, int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getValueAnnotation(String, String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getValues() - Method in class bacnet.datamodel.dataset.ExpressionData
getValues() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
getValues() - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
getValues() - Method in class bacnet.table.core.ColorMapper
getValues() - Method in class bacnet.table.core.ColorMapperRCP
getValues(String) - Method in class bacnet.datamodel.annotation.CodonUsage
getVar() - Method in class bacnet.table.core.ColorMapper
getVar() - Method in class bacnet.table.core.ColorMapperRCP
getVariance() - Method in class bacnet.datamodel.dataset.ExpressionData
getVarianceValue(String) - Method in class bacnet.datamodel.dataset.GeneExpression: Get variance value of corresponding probe in double[][] values
getVertices() - Method in class bacnet.datamodel.dataset.Network: List of vertices = genome elements + their attributes = genome position, type, annotation
getViewedSequence() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
getViewedSequence() - Method in interface org.biojava3.core.sequence.template.SequenceView
getViewId() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
getViewId() - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
getViewId() - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
getViewId() - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
getViewId() - Method in class bacnet.sequenceTools.SrnaView
getViewID() - Method in class bacnet.sequenceTools.AnnotationView
getViewID() - Method in class bacnet.sequenceTools.GeneView
getVoidMatrix() - Static method in class bacnet.datamodel.dataset.ExpressionMatrix: Create a matrix containing only one element = MISSING_VALUE
getWebpageTitle() - Method in class bacnet.Database
getWGS(ArrayList<String>) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Extract all WGS (Whole Genome Shotgun) from genomesList
getWidth() - Method in class bacnet.genomeBrowser.core.Region
getWidth() - Method in class bacnet.table.core.MatrixSize
getWidthBP() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
getWidthBP() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
getWidthDefault() - Method in class bacnet.table.core.MatrixSize
getWidthRowNameDefault() - Method in class bacnet.table.core.MatrixSize
getWindowSize() - Method in class org.biojava3.core.sequence.views.WindowedSequence: Access the current window size
getWurtzelInfo() - Static method in class bacnet.scripts.listeriomics.srna.SrnaTables: Read the different tables from Wurtezel, Sesto et al. 2012 publication and create a list of sRNAs from the different tables
getX1() - Method in class bacnet.genomeBrowser.core.Region
getX2() - Method in class bacnet.genomeBrowser.core.Region
getY1() - Method in class bacnet.genomeBrowser.core.Region
getY2() - Method in class bacnet.genomeBrowser.core.Region
getZoom() - Method in class bacnet.genomeBrowser.core.Track
getZoomHeightMax() - Method in class bacnet.genomeBrowser.core.Zoom: Maximal value for the zoom
getZoomHeightPosition() - Method in class bacnet.genomeBrowser.core.Zoom: Position of the zoom for height
getZoomNumber() - Method in class bacnet.genomeBrowser.core.Zoom
getZoomPosition() - Method in class bacnet.genomeBrowser.core.Zoom
getZoomRatio() - Method in class bacnet.genomeBrowser.core.Zoom
getZoomVertical() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
GFF_ATTRIBUTES - Static variable in class bacnet.reader.GFFNCBIReader
GFF3Reader - Class in org.biojava3.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GFF3Reader() - Constructor for class org.biojava3.genome.parsers.gff.GFF3Reader
GFF3Writer - Class in org.biojava3.genome.parsers.gff
GFF3Writer() - Constructor for class org.biojava3.genome.parsers.gff.GFF3Writer
GFFNCBIReader - Class in bacnet.reader: Read GFF files to create a Genome object
GFFNCBIReader() - Constructor for class bacnet.reader.GFFNCBIReader
GlaserFCannotation - Class in bacnet.datamodel.annotation
GlaserFCannotation() - Constructor for class bacnet.datamodel.annotation.GlaserFCannotation
GluC_Actino_Insoluble - Enum constant in enum bacnet.datamodel.proteomics.NTerm.ExperimentName
GluC_Actino_Soluble - Enum constant in enum bacnet.datamodel.proteomics.NTerm.ExperimentName
gradientColor(int) - Static method in class bacnet.utils.BasicColor
GRAPH_NAME - Static variable in class bacnet.e4.rap.SynTView
GRAPH_NAME - Static variable in class bacnet.views.CoExprNetworkView
GREEN - Static variable in class bacnet.utils.BasicColor
GREY - Static variable in class bacnet.utils.BasicColor
GRNormalization - Class in bacnet.scripts.core.normalization
GRNormalization() - Constructor for class bacnet.scripts.core.normalization.GRNormalization
group() - Method in class org.biojava3.genome.parsers.gff.Feature: Get the first item (everything before first semicolon, if it has one) in the attribute field, which is assumed to be a group identifer.
group() - Method in interface org.biojava3.genome.parsers.gff.FeatureI: Get the group id of the feature.
GroupLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(int, int, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
GroupLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.GroupLocation
groupValues() - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a collection of all unique group ids in the list, as defined by the group() method of the features.
GZIP_MAGIC - Static variable in class org.biojava3.core.util.InputStreamProvider: The magic number found at the start of a GZIP stream.

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