C-Index

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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

C

C_nk(int, int) - Static method in class bacnet.utils.MathUtils: Calculate the combination C_nk
CACHE_PROPERTY - Static variable in class org.biojava3.core.util.InputStreamProvider
calc(Comparison) - Static method in class bacnet.scripts.database.ComparisonsCreation: Run the comparison by calculating statistical parameters given in tests ArrayList
calcEnergy(String) - Static method in class bacnet.scripts.core.UNAfold: From a bunch of stochast folding, generate a list of Free Energies
calcEnergy(String) - Static method in class bacnet.utils.UNAfold: From a bunch of stochast folding, generate a list of Free Energies
calcFilterAndSave(ArrayList<String>, String, String, ArrayList<Filter>, boolean, boolean) - Static method in class bacnet.scripts.database.ComparisonsCreation: Calculate a comparison, filter the results, and save ExpressionMatrix and list of elements up-regulated and down-regulated
calcGeneCNV() - Static method in class bacnet.scripts.database.DNASeqCreation: For each RNAseq and Sequence element, calculate the mean value of copy number variation THIS NEED TO BE RUN AFTER CONVERSION of RNASeq files
calcGenExprTilingComparisons(Experiment) - Static method in class bacnet.scripts.listeriomics.TilingGeneExprDataBase: Calculate GeneExpr and Tiling comparisons files
calcP(double[], double[], PolynomialSplineFunction, PolynomialSplineFunction) - Static method in class bacnet.scripts.core.stat.LPE
calculate(String) - Method in class bacnet.datamodel.annotation.CodonUsage: Calculate Codon usage of a sequence
Providing codonTable has been loaded first
calculateComparison(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Febit: Calculate Log of Fold Change (mean difference) for each value, and p-value
calculateComparison(String, String) - Static method in class bacnet.scripts.listeriomics.technology.LT: Calculate Log of Fold Change (mean difference) for each value, and p-value
calculateComparison(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Macroarray: Calculate Log of Fold Change (mean difference) for each value, and p-value
calculateComparison(String, String) - Static method in class bacnet.scripts.listeriomics.technology.NimbleGen: Calculate Log of Fold Change (mean difference) for each value, and p-value
calculateComparison(String, String, boolean) - Static method in class bacnet.scripts.listeriomics.technology.Agilent: Calculate Log of Fold Change (mean difference) for each value, and p-value
calculateComparison(String, String, boolean) - Static method in class bacnet.scripts.listeriomics.technology.UGiessen: Calculate Log of Fold Change (mean difference) for each value, and p-value
calculateCompMatrix(ArrayList<String>, ArrayList<String>, boolean, boolean) - Static method in class bacnet.scripts.database.ComparisonsCreation: Calculate a list of comparisons
calculateIdentities() - Method in class bacnet.scripts.blast.BlastResult
calculateMiddle() - Method in class bacnet.genomeBrowser.core.Region
calculateOneSDProfile(Genome, int, int, Strand, String) - Static method in class bacnet.scripts.genome.SDProfile
calculateSDProfile(Genome) - Static method in class bacnet.scripts.genome.SDProfile
calculateSize() - Method in class bacnet.genomeBrowser.core.Region
calculateStartCodonProfile(Genome, String, int) - Static method in class bacnet.scripts.genome.StartCodonProfile: Create an NGS data where:
Start codon represent a coverage of 10 Stop codon represent a coverage of 5 every other codon a coverage of 0
calcVarM(ExpressionMatrix, double[]) - Static method in class bacnet.scripts.core.stat.LPE
calcZ(double[], double[], PolynomialSplineFunction, PolynomialSplineFunction) - Static method in class bacnet.scripts.core.stat.LPE
calcZoomNumber() - Method in class bacnet.genomeBrowser.core.Zoom
calcZoomRatio() - Method in class bacnet.genomeBrowser.core.Zoom: We have MINMIAL_BP_NB * zoomRatio^zoomNumber = totalBP
So: zoomRatio = (totalBP/MIN_NB_BP)^(1/zoomNumber)
CaseInsensitiveCompound - Class in org.biojava3.core.sequence.transcription: Attempts to wrap compounds so it is possible to view them in a case insensitive manner
CaseInsensitiveCompound(NucleotideCompound) - Constructor for class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
CaseInsensitiveTriplet(NucleotideCompound, NucleotideCompound, NucleotideCompound) - Constructor for class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
CasePreservingProteinSequenceCreator - Class in org.biojava3.core.sequence.io: A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.
CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator
CDSComparator - Class in org.biojava3.core.sequence
CDSComparator() - Constructor for class org.biojava3.core.sequence.CDSComparator
CDSSequence - Class in org.biojava3.core.sequence: Represents a exon or coding sequence in a gene.
CDSSequence(TranscriptSequence, int, int, int) - Constructor for class org.biojava3.core.sequence.CDSSequence
centerColumn(double[][]) - Static method in class bacnet.utils.ArrayUtils: Center all the column from the Matrix
centerRow(double[][]) - Static method in class bacnet.utils.ArrayUtils: Center all the row from the Matrix
checksum(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Performs a simple CRC64 checksum on any given sequence.
CHROMO - Static variable in class bacnet.raprcp.NavigationManagement
Chromosome - Class in bacnet.datamodel.sequence: A ChromosomeSequence is a DNASequence but keeps track of geneSequences
Chromosome() - Constructor for class bacnet.datamodel.sequence.Chromosome
Chromosome(String) - Constructor for class bacnet.datamodel.sequence.Chromosome
Chromosome(String, CompoundSet<NucleotideCompound>) - Constructor for class bacnet.datamodel.sequence.Chromosome
Chromosome(SequenceReader<NucleotideCompound>) - Constructor for class bacnet.datamodel.sequence.Chromosome
Chromosome(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class bacnet.datamodel.sequence.Chromosome
CHROMOSOME - Enum constant in enum org.biojava3.core.sequence.DNASequence.DNAType
ChromosomeBacteriaSequence - Class in bacnet.datamodel.sequence: A ChromosomeSequence is a DNASequence but keeps track of geneSequences
ChromosomeBacteriaSequence() - Constructor for class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
ChromosomeBacteriaSequence(String) - Constructor for class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
ChromosomeBacteriaSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
ChromosomeBacteriaSequence(SequenceReader<NucleotideCompound>) - Constructor for class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
ChromosomeBacteriaSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
ChromosomeSequence - Class in org.biojava3.core.sequence: A ChromosomeSequence is a DNASequence but keeps track of geneSequences
ChromosomeSequence() - Constructor for class org.biojava3.core.sequence.ChromosomeSequence: Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction.
ChromosomeSequence(String) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence: String is king and assume DNA
ChromosomeSequence(String, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence: Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
ChromosomeSequence(SequenceReader<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence: Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
ChromosomeSequence(SequenceReader<NucleotideCompound>, CompoundSet<NucleotideCompound>) - Constructor for class org.biojava3.core.sequence.ChromosomeSequence: Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
CIRCOS - Static variable in class bacnet.utils.HTMLUtils
CIRCOS_BACK_PATH - Static variable in class bacnet.datamodel.dataset.Network
CIRCOS_NAME - Static variable in class bacnet.e4.rap.SynTView
CIRCOS_NAME - Static variable in class bacnet.views.CoExprNetworkView
CircularGenomeJPanel - Class in bacnet.scripts.genome: Circular Genome Panel created for displaying Small RNAs in CGView
CircularGenomeJPanel(int, int, Genome, String) - Constructor for class bacnet.scripts.genome.CircularGenomeJPanel: Run circularGenome for Listeriomics Circos network graph
CircularGenomeJPanel(int, int, Srna.TypeSrna) - Constructor for class bacnet.scripts.genome.CircularGenomeJPanel: Create the panel for displaying Srna.
CircularGenomeJPanel(int, int, GenomeNCBI, String) - Constructor for class bacnet.scripts.genome.CircularGenomeJPanel
circularLocation(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper: Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
circularLocation(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools: Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
CisReg - Enum constant in enum bacnet.datamodel.sequence.Srna.TypeSrna
classEqual(Object, Object) - Static method in class org.biojava3.core.util.Equals: This method should be called before beginning any equals methods.
ClasspathResource - Class in org.biojava3.core.sequence.io.util: This object represents a classpath resource on the local system.
ClasspathResource(String) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource: Basic constructor only allowing you to specify where to find the file.
ClasspathResource(String, boolean) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource: Advanced constructor which allows you to optionally pre-cache the data
ClasspathResource(String, boolean, boolean) - Constructor for class org.biojava3.core.sequence.io.util.ClasspathResource: Advanced constructor which lets you set the preCache variable and to force the type of file we are decompressing.
cleanDatabase(String) - Static method in class bacnet.scripts.blast.BlastDatabase: Remove in all genome folders a certain type of file
cleanDataTable() - Static method in class bacnet.scripts.arrayexpress.ArrayExpress: Method to remove the unsued lines in the data files for BUGS and MEXP technologies If those lines remain present it causes failures to create the curated tables with the global method
cleanStringFromHex(String) - Static method in class bacnet.utils.FileUtils: Search hexadecimal code in a String indicated by %
Replace them by they ASCII representation
cleanSVGFile() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics: Clean SVG file to be able to replace strain name by homolog information
Names of strain are created in many different "Text table" in the SVG file which have to be removed
cleanUpDatabase() - Method in class bacnet.Database: Cleanup database when closing the website
cleanUpTempFiles() - Static method in class bacnet.scripts.genome.SDProfile
clear() - Method in class org.biojava3.core.util.FlatFileCache
clear() - Method in class org.biojava3.core.util.SoftHashMap
clearChromosome() - Method in class bacnet.datamodel.sequence.Chromosome: Void a Chromosome when Website is quit USEFUL in Eclipse RAP
clearGenome() - Method in class bacnet.datamodel.sequence.Genome: Clear current genome from JVM by setting it up to a 4 base genome
clickedElement(MouseEvent) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData: Get base-pair position of the clicked element
clickedElement(MouseEvent) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
clone() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
clone() - Method in class bacnet.genomeBrowser.core.Region: Clone the object
clone() - Method in class bacnet.genomeBrowser.core.Zoom: Clone the object
clone() - Method in class bacnet.table.core.ColorMapper
clone() - Method in class bacnet.table.core.ColorMapperList
clone() - Method in class bacnet.table.core.ColorMapperRCP
clone() - Method in class bacnet.table.core.ColorMapperRCPList
clone() - Method in class bacnet.table.core.Filter
clone() - Method in class bacnet.utils.Filter
clone(double[][]) - Static method in class bacnet.utils.ArrayUtils
clone(String[][]) - Static method in class bacnet.utils.ArrayUtils
clone(ArrayList<String>) - Static method in class bacnet.utils.ArrayUtils
clone(TreeMap<String, Integer>) - Static method in class bacnet.utils.ArrayUtils
clonePoint() - Method in class org.biojava3.core.sequence.location.SimplePoint
clonePoint() - Method in interface org.biojava3.core.sequence.location.template.Point: Returns a copy of this point
close() - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead
close() - Method in class org.biojava3.core.util.PrettyXMLWriter
close() - Method in interface org.biojava3.core.util.XMLWriter: Close this XMLWriter, and it's underlying stream.
close(Closeable) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.
closeGenomeViewer(EPartService) - Static method in class bacnet.e4.rap.SessionControl: Test function for closing a Genomeviewer and check if it is kept in JVM
closeTag(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
closeTag(String) - Method in interface org.biojava3.core.util.XMLWriter: Closes an un-qualified element.
closeTag(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
closeTag(String, String) - Method in interface org.biojava3.core.util.XMLWriter: Closes an element
Clostridiales_NWK - Static variable in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
CLUSTALW - Enum constant in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat
CM - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
CMD - Class in bacnet.utils
CMD() - Constructor for class bacnet.utils.CMD
Codon - Class in bacnet.datamodel.sequence: Class for managing triplet of nucleotides.
Allo<s detection of start and stop codons in nucleotide sequences
Codon() - Constructor for class bacnet.datamodel.sequence.Codon
Codon(Table.CaseInsensitiveTriplet) - Constructor for class org.biojava3.core.sequence.transcription.Table.Codon
Codon(Table.CaseInsensitiveTriplet, AminoAcidCompound, boolean, boolean) - Constructor for class org.biojava3.core.sequence.transcription.Table.Codon
CodonCompound - Class in org.biojava3.core.sequence.compound: Define a codon
CodonCompound(NucleotideCompound, NucleotideCompound, NucleotideCompound, boolean) - Constructor for class org.biojava3.core.sequence.compound.CodonCompound
codonDisplay(String) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Read a sequence and separate the codon by a space
This method return teh sequence as a StringColor, so codon might be colorized after
CodonUsage - Class in bacnet.datamodel.annotation: Tools for calculating codon Usage of amino acid sequences
Codon Usage tables came from : http://www.kazusa.or.jp/codon/
CodonUsage(String) - Constructor for class bacnet.datamodel.annotation.CodonUsage: Providing the name of codon Table, it loads the Table and create CodonUsage
codonUsageEGDe() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
CoExprNetworkView - Class in bacnet.views
CoExprNetworkView() - Constructor for class bacnet.views.CoExprNetworkView
CoExprNetworkView.InitNetworkThread - Class in bacnet.views
COGannotation - Class in bacnet.datamodel.annotation
COGannotation() - Constructor for class bacnet.datamodel.annotation.COGannotation
COGMAP - Static variable in class bacnet.datamodel.annotation.COGannotation
COL - Static variable in class bacnet.raprcp.NavigationManagement
COL_NUMBER - Static variable in class bacnet.datamodel.dataset.GeneExpression
COLNAME_REFSEQ - Static variable in class bacnet.scripts.database.GenomesCreation: Name fo the column in which RefSeq FTP url is found
colorBackground - Variable in class bacnet.utils.StringColor
colorForeground - Variable in class bacnet.utils.StringColor
colorizeSequence(String) - Method in class bacnet.datamodel.annotation.CodonUsage
ColorMapper - Class in bacnet.table.core
ColorMapper(Shell) - Constructor for class bacnet.table.core.ColorMapper
ColorMapper.TypeMapper - Enum in bacnet.table.core
ColorMapperList - Class in bacnet.table.core
ColorMapperList() - Constructor for class bacnet.table.core.ColorMapperList
ColorMapperList(ExpressionMatrix, Shell) - Constructor for class bacnet.table.core.ColorMapperList: Create a list of ColorMapper from a matrix
Each column name corresponding to a TypeMapper will be associated to a ColorMapper
ColorMapperRCP - Class in bacnet.table.core
ColorMapperRCP(Shell) - Constructor for class bacnet.table.core.ColorMapperRCP
ColorMapperRCP.Type - Enum in bacnet.table.core
ColorMapperRCPList - Class in bacnet.table.core
ColorMapperRCPList() - Constructor for class bacnet.table.core.ColorMapperRCPList
ColorMapperRCPList(ExpressionMatrix, Shell) - Constructor for class bacnet.table.core.ColorMapperRCPList
ColorMapperWizard - Class in bacnet.table.gui
ColorMapperWizard(ColorMapperList, Shell) - Constructor for class bacnet.table.gui.ColorMapperWizard
ColorMapperWizardPage - Class in bacnet.table.gui
ColorMapperWizardPage(ColorMapper, Shell) - Constructor for class bacnet.table.gui.ColorMapperWizardPage
ColorMapperWizardPage(Shell) - Constructor for class bacnet.table.gui.ColorMapperWizardPage: Create the wizard.
ColorSWT - Class in bacnet.table.core
ColorSWT(int, int, int) - Constructor for class bacnet.table.core.ColorSWT
ColorSWT(Color) - Constructor for class bacnet.table.core.ColorSWT
CombinationGenerator - Class in bacnet.scripts.core.vennDiagram: Class for finding every combination of a set of integer
CombinationGenerator - Class in bacnet.utils
CombinationGenerator(int, int) - Constructor for class bacnet.scripts.core.vennDiagram.CombinationGenerator
CombinationGenerator(int, int) - Constructor for class bacnet.utils.CombinationGenerator
combinator(ArrayList<String>, int) - Static method in class bacnet.scripts.core.vennDiagram.VennDiagram: Create all combinations of k elements of list1
combineMatrices(String, String) - Static method in class bacnet.scripts.listeriomics.technology.UGiessen
COMBO - Static variable in class bacnet.raprcp.NavigationManagement
COMMA - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
compare(ExpressionData, boolean) - Method in class bacnet.datamodel.dataset.ExpressionData: Create Tiling data from the comparison of this one and data2
compare(GeneExpression, boolean) - Method in class bacnet.datamodel.dataset.GeneExpression: Create GeneExpression data from the comparison of this one and data2
compare(NGS, boolean) - Method in class bacnet.datamodel.dataset.NGS: Create RNASeq data from the comparison of this one and data2
compare(Tiling, boolean) - Method in class bacnet.datamodel.dataset.Tiling: Create Tiling data from the comparison of this one and data2
compare(BioCondition, boolean) - Method in class bacnet.datamodel.expdesign.BioCondition: Create a BioCondition containing the different data for comparing this BioCondition to bioCond2
compare(BlastResult, BlastResult) - Method in class bacnet.scripts.blast.BlastResult.BlastResultCompare
compare(CDSSequence, CDSSequence) - Method in class org.biojava3.core.sequence.CDSComparator: Used to sort two CDSSequences where Negative Strand makes it tough
compare(ExonSequence, ExonSequence) - Method in class org.biojava3.core.sequence.ExonComparator
compare(AbstractSequence<?>, AbstractSequence<?>) - Method in class org.biojava3.core.sequence.SequenceComparator
compare(Viewer, Object, Object) - Method in class bacnet.table.core.BioConditionComparator
compare(Viewer, Object, Object) - Method in class bacnet.table.core.TableViewerComparator
compareNTermData(String, String) - Static method in class bacnet.datamodel.proteomics.NTermUtils: Return the list of NTerm common to both experiment
NTerm are equal if:
same peptide sequence same modification
compareTo(Point) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
compareTo(Point) - Method in class org.biojava3.core.sequence.location.SimplePoint
Comparison - Class in bacnet.scripts.core
Comparison() - Constructor for class bacnet.scripts.core.Comparison
Comparison(ArrayList<StatTest>, ArrayList<String>, ArrayList<String>, boolean) - Constructor for class bacnet.scripts.core.Comparison: Create a Comparison object used in Statistical comparison case
ComparisonAtlas - Class in bacnet.expressionAtlas.core: A ComparisonAtlas is related to a Comparison object and gives the list of genome elements over, under and not differentially expressed
ComparisonAtlas() - Constructor for class bacnet.expressionAtlas.core.ComparisonAtlas
ComparisonAtlas(ExpressionMatrix, ArrayList<String>, String, Filter) - Constructor for class bacnet.expressionAtlas.core.ComparisonAtlas: For a specific biological condition comparison update the list of genome elements 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
ComparisonsCreation - Class in bacnet.scripts.database
ComparisonsCreation() - Constructor for class bacnet.scripts.database.ComparisonsCreation
COMPARTMENT_NAMES - Static variable in class bacnet.datamodel.annotation.SubCellCompartment
ComplementCompound - Interface in org.biojava3.core.sequence.template
ComplementSequenceView<C extends ComplementCompound> - Class in org.biojava3.core.sequence.views: For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g. base A will become base T
ComplementSequenceView(Sequence<C>) - Constructor for class org.biojava3.core.sequence.views.ComplementSequenceView
completeCircularPasses(int, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper: Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
completeCircularPasses(int, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools: Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e. if we have a sequence of length 10 and the location 3..52 we make 4 complete passes through the genome to go from position 3 to position 52.
CompositeNTermInfo - Class in bacnet.genomeBrowser: NTerm composite which is displayed on the right of the GenomeViewer.
CompositeNTermInfo(Composite, int) - Constructor for class bacnet.genomeBrowser.CompositeNTermInfo: Initiate a CompositeNTermInfo
Compound - Interface in org.biojava3.core.sequence.template
CompoundColorization - Class in bacnet.datamodel.sequence
CompoundColorization() - Constructor for class bacnet.datamodel.sequence.CompoundColorization
CompoundNotFoundError - Error in org.biojava3.core.exceptions
CompoundNotFoundError(CharSequence) - Constructor for error org.biojava3.core.exceptions.CompoundNotFoundError
compoundsEqual(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
compoundsEquivalent(C, C) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
compoundsEquivalent(C, C) - Method in interface org.biojava3.core.sequence.template.CompoundSet
compoundsEquivalent(AminoAcidCompound, AminoAcidCompound) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
CompoundSet<C extends Compound> - Interface in org.biojava3.core.sequence.template
compoundToInt(NucleotideCompound) - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
CompoundTranslator<F extends Compound,T extends Compound> - Interface in org.biojava3.core.sequence.template
compute() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
computeTotalList() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
ConcurrencyTools - Class in org.biojava3.core.util: Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
configure(Application) - Method in class bacnet.e4.rap.BasicApplication
configure(Application) - Method in class bacnet.e4.rap.setup.BasicApplication
consistentAccessions(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper: Scans a list of locations and returns true if all the given locations are linked to the same sequence.
containProbe(String) - Method in class bacnet.datamodel.dataset.GeneExpression: Check if TreeMap<String, Integer> probes contains a probe
containProteomes() - Method in class bacnet.datamodel.expdesign.BioCondition
containRNASeq() - Method in class bacnet.datamodel.expdesign.BioCondition
contains(Location) - Method in class org.biojava3.genome.parsers.gff.Location: Check if this location contains the other.
containStopCodon(NTerm, Sequence, int[]) - Static method in class bacnet.datamodel.proteomics.NTermFilter: Return true if it contains a StopCodon between the peptide and the overlaping sequence
containTranscriptomes() - Method in class bacnet.datamodel.expdesign.BioCondition
CONTIG - Enum constant in enum org.biojava3.core.sequence.DNASequence.DNAType
convert(NGS, boolean) - Method in class bacnet.datamodel.dataset.NGS: Run the conversion of wigfiles
convert(Experiment) - Static method in class bacnet.datamodel.dataset.GeneExpression: Read all GeneExpr data and save in GeneExpressionStreaming format
convert(Experiment) - Static method in class bacnet.datamodel.dataset.Tiling: Read Tiling data in Experiment and save in TilingDataStreaming format
convert(Srna) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Convert an Srna into a DNASequence
convertAll() - Static method in class bacnet.datamodel.annotation.Signature: Read all Signature in text files, and serialize them in Database.getSIGNATURES()\*
Save an array with the HashMap between Signature name and ID
convertAll() - Static method in class bacnet.scripts.database.GenomesCreation: Convert all genomes available in the database
convertCoverageFiles(Experiment, boolean) - Static method in class bacnet.scripts.database.NGSCreation: Go through all RNASeq data found in the list BioCondition.getRNASeqBioConditions() and convert all of them
convertData(ExpressionMatrix) - Method in class bacnet.datamodel.dataset.GeneExpression: Convert data from an ExpressionMatrix to a GeneExpression
convertData(ExpressionMatrix) - Method in class bacnet.datamodel.dataset.Tiling
convertDNASequenceGene(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversionElement: From a DNASequence make a Gene object
convertDNASequenceGeneral(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversionElement: From a DNASequence object, create Sequence
Mainly used in GenomeConversion methods
convertDNASequenceNcRNA(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversionElement: From a DNASequence make a Gene object
convertDNASequenceOperon(String[], GenomeNCBI) - Static method in class bacnet.datamodel.sequence.Operon: Take row from Annot_sup table and creat an Operon Object from it
convertDNASequenceOperon(String[], GenomeNCBI) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversionElement
convertHexToString(String) - Static method in class bacnet.utils.FileUtils: Convert an hexadecimal ASCII to a String
convertOuput(String, String, boolean, BlastOutput.BlastOutputTYPE) - Static method in class bacnet.scripts.blast.BlastOutput: Convert asn given by blastResult into out using BlastOutputType
convertProteomicsData(Experiment) - Static method in class bacnet.scripts.database.ProteomicsCreation: Convert all ExpressionMatrix found for Proteomic datasets and save them in Streaming folder
convertStreamToString(InputStream) - Static method in class org.biojava3.core.util.StringManipulationHelper
convertToVennMasterDataList() - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
convertWigFile(NGS, boolean) - Method in class bacnet.datamodel.dataset.NGS: WIG file are common RNASeq data
Calculate first the MEDIAN value of the different replicates ad then log2 transform and save the NGS data Two columns:
one for the base pair position one for the coverage value
convertXtoBP(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData: Convert position in the display to a position in the genome
(inverse function of basepairToXimage(int bpIndex))
If MassSpec data has not been register do it
convertXtoBP(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome: Convert position in the display to a position in the genome
(inverse function of basepairToXimage(int bpIndex))
copy(InputStream, OutputStream) - Static method in class org.biojava3.core.sequence.io.util.IOUtils: Moves the bytes from input to output using a 4KB byte array.
copy(String, String) - Static method in class bacnet.utils.FileUtils: copy file with path=input to file with path=output
copyColumnAt(String, double[]) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
copyFastafile(String, String) - Static method in class bacnet.scripts.database.PhylogenomicsCreation: Copy All 1st chromosome fasta files in fastaFolder and rename them with genome name
copyRowAt(String, double[]) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
copyTranscriptomicsTable() - Static method in class bacnet.scripts.arrayexpress.ArrayExpress: Copy the transcriptomics curated table in the NormData>ExprMatrix folder
CORR - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
CORR - Enum constant in enum bacnet.table.core.ColorMapper.TypeMapper
CORR - Enum constant in enum bacnet.table.core.ColorMapperRCP.Type
CORR_CUTOFF - Static variable in class bacnet.datamodel.dataset.Network
correctResults(String) - Static method in class bacnet.scripts.genome.SDProfile: Data from EGDe SD profile are corrupted need to correct them
Need to inverse result of values after the 1710999 base pair

IMPORTANT: Run only one time 13/01/2014
correspondingMassSpecData(NTerm) - Method in class bacnet.genomeBrowser.core.Track: Return the MassSpecData where an Nterm can be found
countAT(Sequence<NucleotideCompound>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Returns the count of AT in the given sequence
countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
countCompounds(C...) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Counts the number of times a compound appears in this sequence store
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
countCompounds(C...) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Delegates to SequenceMixin#countCompounds(org.biojava3.core.sequence.template.Sequence, C[])
countCompounds(C...) - Method in class org.biojava3.core.sequence.template.AbstractSequence
countCompounds(C...) - Method in interface org.biojava3.core.sequence.template.Sequence: Returns the number of times we found a compound in the Sequence
countCompounds(C...) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
countCompounds(Sequence<C>, C...) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence
countGC(Sequence<NucleotideCompound>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Returns the count of GC in the given sequence
countRTerminal(String) - Static method in class bacnet.datamodel.proteomics.NTermUtils: Count the number of peptides with an R (arginine), and finishing with an R
covariance(double[], double[]) - Static method in class bacnet.utils.VectorUtils: Calculate the covariance of x * y
covarianceMatrix(double[][]) - Static method in class bacnet.utils.ArrayUtils: Calcul of the covariance Matrix
CP - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
CRC64Checksum - Class in org.biojava3.core.util: Utility class that calculates a CRC64 checksum on a stream of bytes.
CRC64Checksum() - Constructor for class org.biojava3.core.util.CRC64Checksum
create() - Method in class bacnet.e4.rap.BacnetE4PointFactory
create() - Method in class bacnet.e4.rap.setup.BacnetE4PointFactory
createAll(Experiment) - Static method in class bacnet.expressionAtlas.core.ComparisonAtlas: For each comparison create a Comparison object containing the list of all differentially expressed genes, sRNAs, asRNAs, and cisRegs

WANRING: OrganizeDatabase.organizeComparisonsData(exp) as to be run first!!!
createAllCompMatrix(ArrayList<String>) - Static method in class bacnet.scripts.database.ComparisonsCreation: Go through all comparisons and create for each Tiling and GenExpression different matrices giving the number of genes, Srna and asRNA overexpressed and underexpressed
createAnnotation() - Method in class bacnet.datamodel.dataset.NTermData: Create an Annotation Table from the list of Nterm
createAnnotation(Genome, String) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversion: Create a Table with all elements of the Genome, which will be used for element search and display on the GenomeViewer
createArrayExpressTable() - Static method in class bacnet.scripts.arrayexpress.ArrayExpress: Create a new txt file containing all the accession data for every file to download
createArrayTable() - Static method in class bacnet.scripts.arrayexpress.ArrayExpress: Create a txt file giving the name of each array technology
createASrnaTSStable() - Static method in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics: Run different function to curate the data given by Omri 15/11/2012
createBioCondition(String) - Static method in class bacnet.datamodel.proteomics.NTermCreateData: Create a BioCondition containing only one Nterm
createBioConditionFigure(boolean) - Static method in class bacnet.scripts.listeriomics.SummaryListeriomics: Create the different element for the figure representing the BioCondition
createBlastCommands(String, double) - Static method in class bacnet.scripts.database.HomologCreation: Launch blast commands creation
createBlastCommands(String, String, String, ArrayList<String>, double) - Static method in class bacnet.scripts.database.HomologCreation: Create .bat files with the command lines for each blast.
createBlastDatabases(String, String[], boolean, boolean) - Static method in class bacnet.scripts.blast.Blast: Create blast database for each genome contained in GenomeFolder !!!!!!!!!!
createBlastDatabases(String, String, ArrayList<String>) - Static method in class bacnet.scripts.database.HomologCreation: Create blast database for each genome contained in genomesInput
createBlastDB() - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: Create blastP databases
createBlastDB(String) - Static method in class bacnet.scripts.blast.BlastDatabase: Create blastP databases
createBlastDB(String) - Static method in class bacnet.scripts.database.HomologCreation: Create blastP databases
createBlastScript(String) - Static method in class bacnet.scripts.database.HomologCreation: Creation of the general command file that will be used to create the ones for each blast
createBlastSmallORFDB() - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: Create blastP databases
createBlastSmallORFDB(String) - Static method in class bacnet.scripts.blast.BlastDatabase: Create blastP databases
createCircularGenomeView(Genome, String) - Static method in class bacnet.scripts.database.GenomesCreation: Deprecated.
createCoExpressionNetwork(ArrayList<String>, String) - Static method in class bacnet.scripts.database.NetworkCreation: Create Co-Expression network for all absolute expression dataset of a specific genome
createCoExprTable(String) - Static method in class bacnet.scripts.database.NetworkCreation: Create Database.getInstance().getCoExprNetworkArrayPath() with all co-expression network available
Then for each genome available create a file with list of datasets available for co-expression network creation. this will be saved in Database.getLISTDATA_COEXPR_NETWORK_TRANSCRIPTOMES_PATH() + "_" + genomeName + ".txt"
createCOGNumberEGDe() - 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
createComparisonsTable() - Static method in class bacnet.scripts.arrayexpress.ArrayExpress: Use the BioConditions and the curated sdrf files from ArrayExpressRawData folders to create a Comparison table
createConservationTables() - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Read Srna.PATH_CONSERVATION table and display it in HeatMapView
Headers are reorganized by their phylogeny positions
createConservationTables10403S() - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Read sRNAConservation10403S.txt table and display it in HeatMapView
Headers are reorganized by their phylogeny positions
createControl(Composite) - Method in class bacnet.table.gui.ColorMapperWizardPage: Create contents of the wizard.
createControls(Composite) - Method in class bacnet.e4.rap.setup.SetupPart: Create contents of the view part.
createControls(Composite) - Method in class bacnet.e4.rap.TestPart: Create contents of the view part.
createControls(Composite) - Method in class bacnet.views.CRISPRPredictView: Create contents of the view part.
createControls(Composite) - Method in class bacnet.views.CRISPRPredictView2: Create contents of the view part.
createDatabase() - Static method in class bacnet.scripts.listeriomics.srna.SmallPeptidesSearch: Deprecated.

Create database file which contains all genome available
This genome list contains all the genomes from GenomeFolder and all the genome contained in GenomePhylogeny.PATH_TABLE (=All bacteria phylogeny)
createDatabase() - Static method in class bacnet.scripts.listeriomics.srna.Srna10403SOliver: Create database file which contains all genome available
It will be used by Blast afterwards

BE CAREFULL THAT THESE GENOMES HAVE BEEN ESTABLISHED FOR BLAST SEARCH (=database is created through Blast.createBlastDatabases();)
createDatabaseForORF() - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: Create a fasta file with all proteins from the different chromosomes Using faa file create blast Verify by looking at all file size
createDatabaseForORF(String) - Static method in class bacnet.scripts.blast.BlastDatabase: Create a fasta file with all proteins from the different chromosomes Using faa file create blast Verify by looking at all file size
createDatabaseForSmallORF() - Static method in class bacnet.scripts.blast.BlastDatabase: translate every genomes on the 6 frames Create a fasta file with all proteins from the different chromosomes Using faa file create blast Verify by looking at all file size
createDatabaseForSmallORF() - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: translate every genomes on the 6 frames Create a fasta file with all proteins from the different chromosomes Using faa file create blast Verify by looking at all file size
createDataBases() - Static method in class bacnet.scripts.blast.ProteinTools: Create:
Protein DB UTR DB fusion Protein DB and Protein DB Genome DB TIS DB
createDataBases() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: Create:
Protein DB UTR DB fusion Protein DB and Protein DB Genome DB TIS DB
createDialogArea(Composite) - Method in class bacnet.expressionAtlas.core.SelectGenomeElementDialog: Create contents of the wizard.
createEdgeWT() - Static method in class bacnet.scripts.core.normalization.GRNormalization: By copying GENERAL_WT_DATA create GENERAL_WT_NAME tiling data
createEGDeAverage() - Static method in class bacnet.datamodel.dataset.EGDeWTdata: From the list of Wild Type data given by EGDeWTdata.wildTypes calculate the mean and save it
createEGDeGenomeElementList() - Static method in class bacnet.scripts.database.GenomesCreation: Create a list of all Genes, all ASrnas, and all CisRegs of EGD-e
Srnas list is already created in EGDe_SRNA_PATH
createEstimates(TreeMap<String, GeneExpression>) - Static method in class bacnet.scripts.core.stat.LPE: For each comparison calculate the LPE estimate, by creating a matrix of all expression values and estimates LPE using each of these matrices
createExpressionMatrix(Genome) - Method in class bacnet.scripts.core.Expression: Combine all Transcriptomes describe in Expression data, and return the combine ExpressionMatrix
createFAA(String) - Static method in class bacnet.scripts.database.HomologCreation: Create a FAA file in the BLASTDB folder for each genome.
createFastaAA() - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: Create blastP databases
createFastaAA(String) - Static method in class bacnet.scripts.blast.BlastDatabase: Create blastP databases
createFastaAASmallORF() - Static method in class bacnet.scripts.blast.BlastDatabase: Extract result and create fasta files
createFastaAASmallORF() - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: Extract result and create fasta files
createFilecatsTable(BioCondition, String, boolean) - Static method in class bacnet.scripts.core.normalization.GRNormalization: Create filecats = list of data in a table, used by the R script to run Tiling normalization
createFinalList() - Static method in class bacnet.scripts.listeriomics.srna.SrnaFinalList: Read the different :list from different publication and combine all of them into an Srna final list
Every table should be found in SrnaTables.PATH
createFolderCopyFNA(String, String) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversion: Create a folder for each Genome, and copy all .fna in it
createFoldingFigures() - Static method in class bacnet.scripts.listeriomics.srna.SrnaFinalList: Run UNAFold for each sRNA to calculate folding
Copy each .png image from UNAFold folder to Srna.PATH_SEC_STRUCTURE
createGenBankFile(Genome, String) - Static method in class bacnet.reader.GBKReader: Create GenBank file with first chromosome
TO BE FIXED for adding other chromosomes
createGeneHashMap() - Method in class bacnet.datamodel.dataset.NTermData: Regroup NTerm using genes of EGD-e
Each EGD-e gene will be associated to a list of NTerm overlapping it
Fill: HashMap<String, ArrayList>() aTISMap, HashMap<String, ArrayList>() genes, HashMap<String, ArrayList>() geneModification
createGenomeDB() - Static method in class bacnet.scripts.blast.ProteinTools: lists of small peptides contained in the genome of EGDe on 6frames.
The small peptides include in the list are the one only of size more than 5aa, and surrounded by at least one R.
example: Start - peptide - R
Stop - peptide - R

Element like: Start - peptide - Stop are rejected from the analysis

frame 1 = EGDe genome, ID=genome frame 2 = EGDe genome 1bp on the left, ID=genomeM frame 3 = EGDe genome 1bp on the right, ID=genomeP frame 4 = EGDe reverse complement genome, ID=genomeCompl frame 5 = EGDe reverse complement genome 1bp on the left, ID=genomeComplM frame 6 = EGDe reverse complement genome 1bp on the right, ID=genomeComplP
createGenomeDB() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: lists of small peptides contained in the genome of EGDe on 6frames.
The small peptides include in the list are the one only of size more than 5aa, and surrounded by at least one R.
example: Start - peptide - R
Stop - peptide - R

Element like: Start - peptide - Stop are rejected from the analysis

frame 1 = EGDe genome, ID=genome frame 2 = EGDe genome 1bp on the left, ID=genomeM frame 3 = EGDe genome 1bp on the right, ID=genomeP frame 4 = EGDe reverse complement genome, ID=genomeCompl frame 5 = EGDe reverse complement genome 1bp on the left, ID=genomeComplM frame 6 = EGDe reverse complement genome 1bp on the right, ID=genomeComplP
createGenomeTable() - Static method in class bacnet.scripts.listeriomics.SummaryListeriomics: Create Table 1 for Listeriomics paper with the list of Genomes and different infos
Save in: Project.getPath()+"Table 1 - Genomes.txt"
createGenomeTable(String) - Static method in class bacnet.scripts.database.GenomesCreation: Create Table 1 with the list of Genomes and different infos
Save in: Project.getPath()+"Table 1 - Genomes.txt"
createHashMap() - Method in class bacnet.datamodel.dataset.NTermData: Regroup in different HashMap the NTerm
Fill:
HashMap<String, ArrayList> peptides is to make a simple HashMap between NTerm sequence and a list of corresponding NTerm HashMap<String, ArrayList> modifications links Nterm position to a list of corresponding NTerm
createHomologTable(String) - Static method in class bacnet.scripts.database.HomologCreation: Create all homolog tables for each genome
3 different log files are saved
TabDelimitedTableReader.saveTreeSet(proteinNotFound, GenomeNCBI.PATH_HOMOLOGS + "ProteinNotfFound.homologs.txt");
TabDelimitedTableReader.saveTreeSet(noHomologs, GenomeNCBI.PATH_HOMOLOGS + "NoHomologsFound.homologs.txt");
TabDelimitedTableReader.saveTreeSet(lowHomologs, GenomeNCBI.PATH_HOMOLOGS + "LowHomologsFound.homologs.txt");
createHTMLPageSummary() - Static method in class bacnet.scripts.arrayexpress.ArrayExpressTechnology: Read TABLE_PATH and create an HTML table from it to ease accession to ArrayExpress info
createHTMLPageSummary() - Static method in class bacnet.scripts.database.ProteomicsCreation: DATA_TABLe has been created from a copy paste of ArrayExpress search results.
createHTMLPageSummary() - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressListeriomics: DATA_TABLe has been created from a copy paste of ArrayExpress search results.
createHTMLPageSummary() - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology: Read TABLE_PATH and create an HTML table from it to ease accession to ArrayExpress info
createHTMLPageSummary() - Static method in class bacnet.scripts.listeriomics.ArrayExpressListeriomics: DATA_TABLe has been created from a copy paste of ArrayExpress search results.
createInferiorAbsFilter(double) - Method in class bacnet.table.core.Filter
createInferiorAbsFilter(double) - Method in class bacnet.utils.Filter
createInferiorFilter(double) - Method in class bacnet.table.core.Filter
createInferiorFilter(double) - Method in class bacnet.utils.Filter
createInfoNodes() - Static method in class bacnet.scripts.phylogeny.PhylogenyTools
createIterator(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.
createListeriomicsTable(String) - Static method in class bacnet.scripts.listeriomics.nterm.NTermMain
createListeriomicsTSSTermSeq() - Static method in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics: Create TSS (Transcription Start Site) and TermSeq wig files
createLogFCMatrix(Experiment, Genome) - Static method in class bacnet.scripts.database.ComparisonsCreation: Create Database.logFCMatrix by regrouping every logFC values for genes, sRNAs, asRNAs, and cisRegs in every BioCondition given Experiment
createLogFCMatrix(Experiment, Genome) - Static method in class bacnet.scripts.database.TranscriptomesCreation: Create Database.logFCMatrix by regrouping every logFC values for genes, sRNAs, asRNAs, and cisRegs in every BioCondition given Experiment
createLogFCMatrix(Experiment, String) - Static method in class bacnet.scripts.database.ProteomicsCreation: Create a table will all protein expression for each Genome
createLogfcTranscriptomeTable(ArrayList<String>, String, boolean) - Static method in class bacnet.scripts.database.TranscriptomesCreation: Create LogFC summary matrix for transcriptomics datasets
createMatrix(String, String) - Static method in class bacnet.scripts.listeriomics.technology.JCVI
createMatrixFromTISData() - Static method in class bacnet.scripts.database.ProteomicsCreation: Create a matrix from TIS data for which each gene has its corresponding number of spectra
createMatrixFromTISData() - Static method in class bacnet.scripts.listeriomics.MainListeriomics: Create a matrix from TIS data for which each gene has its corresponding number of spectra
createMDB() - Static method in class bacnet.scripts.blast.ProteinTools
createMDB() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase
createMissingFolders() - Static method in class bacnet.scripts.database.DataFolder
createPartControl(Composite) - Method in class bacnet.e4.rap.BannerView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.e4.rap.InitViewBacnet
createPartControl(Composite) - Method in class bacnet.e4.rap.InitViewListeria
createPartControl(Composite) - Method in class bacnet.e4.rap.InitViewListeriaSample
createPartControl(Composite) - Method in class bacnet.e4.rap.InitViewYersinia
createPartControl(Composite) - Method in class bacnet.e4.rap.SynTView
createPartControl(Composite) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.expressionAtlas.HeatMapProteomicsView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.expressionAtlas.ProteomicsExpressionView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.expressionAtlas.ProteomicsView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.expressionAtlas.TranscriptomicsView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.genomeBrowser.NTerminomicsView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.sequenceTools.AnnotationView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.sequenceTools.GeneView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.sequenceTools.GenomicsView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.sequenceTools.SrnaSummaryView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.sequenceTools.SrnaView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.table.TableSWTView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.views.BannerView: Create contents of the view part.
createPartControl(Composite) - Method in class bacnet.views.CoExprNetworkView
createPartControl(Composite) - Method in class bacnet.views.InitView
createPartControl(Composite) - Method in class bacnet.views.InternalBrowser
createPhylogenomicFigure(String) - Static method in class bacnet.scripts.database.PhylogenomicsCreation: Method to create a Phylogenomic figure using:
JolyTree - https://gitlab.pasteur.fr/GIPhy/JolyTree for alignment and tree construction
FigTree for Drawing Phylogenomic tree
createPhylogenyFile(ArrayList<Sequence>) - Static method in class bacnet.scripts.blast.PhylogenySmallORFs: reading filtered table and create fasta file, assuming that Lite.excel table have been reduced manually by removing doublons
createPhylogenyFile(ArrayList<Sequence>) - Static method in class bacnet.scripts.phylogeny.PhylogenySmallORFs: reading filtered table and create fasta file, assuming that Lite.excel table have been reduced manually by removing doublons
createProbeList() - Static method in class bacnet.datamodel.dataset.GeneExpression: Read general GeneExpression data and extract the list of probes from it
createProbeList() - Static method in class bacnet.datamodel.dataset.Tiling: Read WildType tiling data and extract the list of probes from it
createProteinDB() - Static method in class bacnet.scripts.blast.ProteinTools: Create a fasta file which will be used has a database
This file contains: all genes all new genes described in RAST all Srna on 3 frames all ASrna on 3 frames (300bp long) lists of Genes, ID=lmo, directly taken from NCBI lists of "new"Gene, ID=rastlmo, from the analysis of annotation I just did using RAST software lists of Srna, ID=rli, rliM, rliP, we don't know where is the begining so we have 3 frame for each rli, we start at the first start codon, plus we cut when we found stop codon and peptide smaller than 5aa. lists of ASrna, ID=anti, antiM, antiP, we don't know where is the begining so we have 3 frame for each asRNA, we start at the first start codon, plus we cut when we found stop codon and peptide smaller than 5aa.
createProteinDB() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: Create a fasta file which will be used has a database
This file contains: all genes all new genes described in RAST all Srna on 3 frames all ASrna on 3 frames (300bp long) lists of Genes, ID=lmo, directly taken from NCBI lists of "new"Gene, ID=rastlmo, from the analysis of annotation I just did using RAST software lists of Srna, ID=rli, rliM, rliP, we don't know where is the begining so we have 3 frame for each rli, we start at the first start codon, plus we cut when we found stop codon and peptide smaller than 5aa. lists of ASrna, ID=anti, antiM, antiP, we don't know where is the begining so we have 3 frame for each asRNA, we start at the first start codon, plus we cut when we found stop codon and peptide smaller than 5aa.
createProteolyseMap() - Method in class bacnet.datamodel.dataset.NTermData: Regroup peptides which overlap -> the assumption is that they come from the same protein but were created from proteolyse
createProteomeTable(ArrayList<String>, String) - Static method in class bacnet.scripts.database.ProteomicsCreation: Create Expression summary matrix for proteomics datasets
createPTTandFAAFiles() - Static method in class bacnet.scripts.database.GenomesCreation: Some genomes have been downloaded without PTT files so we create them
PTT files are used by SynTVIew software
createResourceLoader(String) - Static method in class bacnet.e4.rap.BasicApplication
createSequence(Sequence<F>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
createSequence(Sequence<F>) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
createSequence(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
createSequence(Sequence<NucleotideCompound>, Frame) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator
createSequences(Sequence<F>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
createSequences(Sequence<F>) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.DNAToRNATranslator: Overloaded local version which delegates to an optional translator when told to (specified during construction).
createSequences(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator: Performs the core conversion of RNA to Peptide.
createStatMatrix(Experiment, Genome) - Static method in class bacnet.scripts.database.ComparisonsCreation: Create Database.statTable by calculating stat values for genes, sRNAs, and asRNAs in every BioCondition
For genes we use FDRBY calculated from GebneExpression array
For sRNAs and asRNAs we use TSTUDENTTILING for Tiling array
createStatMatrix(Experiment, Genome) - Static method in class bacnet.scripts.database.TranscriptomesCreation: Create Database.statTable by calculating stat values for genes, sRNAs, and asRNAs in every BioCondition
For genes we use FDRBY calculated from GebneExpression array
For sRNAs and asRNAs we use TSTUDENTTILING for Tiling array
createStochasticMatrix(int, int) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
createSubSequence(Sequence<C>, int, int) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Creates a simple sub sequence view delimited by the given start and end.
createSummaryProteomesComparisonsTable() - Static method in class bacnet.scripts.database.BioConditionCreation: Create a table will all main information on the different Comparison of proteomic available
This table will be loaded by BioConditionView
createSummaryProteomesTable() - Static method in class bacnet.scripts.database.BioConditionCreation: Create a table will all main information on the different BioCondition available
This table will be loaded by BioConditionView
createSummaryTables() - Static method in class bacnet.scripts.listeriomics.srna.SrnaFinalList: Create SUmmary Tables for the website
WARNING: GenomeConversion has to be run before!
createSummaryTranscriptomesComparisonsTable() - Static method in class bacnet.scripts.database.BioConditionCreation: Create a table will all main information on the different BioCondition available
This table will be loaded by BioConditionView
createSummaryTranscriptomesTable() - Static method in class bacnet.scripts.database.BioConditionCreation: Create a table will all main information on the different BioCondition available
This table will be loaded by BioConditionView
createSuperiorAbsFilter(double) - Method in class bacnet.table.core.Filter
createSuperiorAbsFilter(double) - Method in class bacnet.utils.Filter
createSuperiorFilter(double) - Method in class bacnet.table.core.Filter
createSuperiorFilter(double) - Method in class bacnet.utils.Filter
createSuperiorFilter(double, double) - Method in class bacnet.table.core.Filter
createSuperiorFilter(double, double) - Method in class bacnet.utils.Filter
createTargetsTable(BioCondition, String) - Static method in class bacnet.scripts.core.normalization.GENormalization
createTechnologiesTable() - Static method in class bacnet.scripts.arrayexpress.ArrayExpress
createTechnoTable() - Static method in class bacnet.scripts.arrayexpress.ArrayExpressTechnology: Create a table with different info about Array Design: Name, number of data which use it
createTechnoTable() - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology: Create a table with different info about Array Design: Name, number of data which use it
createTISDB() - Static method in class bacnet.scripts.blast.ProteinTools: Create database of all peptide from a start codon (M=ATG, L=TTG, V=GTG), to the next stop codon or R
createTISDB() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: Create database of all peptide from a start codon (M=ATG, L=TTG, V=GTG), to the next stop codon or R
createUTRDB() - Static method in class bacnet.scripts.blast.ProteinTools: Create a database with all UTR from Wurtzel et al. 2012
Found here : DATABASE+"table_s1_tss_table.txt"
We found the correct frame so we are sure to have the start codon of the gene at the exact position of NCBI annotation We start at the first start codon, then if stop codon are found in the UTR region we cut in different peptides, remove ones < 5aa, and paste to the last part of the UTR the whole gene amino acide sequence all gene, ID=lmo_n n being the id of the UTR peptide extracted
createUTRDB() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: Create a database with all UTR from Wurtzel et al. 2012
Found here : DATABASE+"table_s1_tss_table.txt"
We found the correct frame so we are sure to have the start codon of the gene at the exact position of NCBI annotation We start at the first start codon, then if stop codon are found in the UTR region we cut in different peptides, remove ones < 5aa, and paste to the last part of the UTR the whole gene amino acide sequence all gene, ID=lmo_n n being the id of the UTR peptide extracted
createValues(int, int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
CRISPRGO_PROJECT - Static variable in class bacnet.Database: Static variable to discriminate Listeriomics project from the others
CRISPRPredictView - Class in bacnet.views
CRISPRPredictView() - Constructor for class bacnet.views.CRISPRPredictView
CRISPRPredictView2 - Class in bacnet.views
CRISPRPredictView2() - Constructor for class bacnet.views.CRISPRPredictView2
CS - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
ct_energy - Static variable in class bacnet.scripts.core.UNAfold
ct_energy - Static variable in class bacnet.utils.UNAfold
ct_prob - Static variable in class bacnet.scripts.core.UNAfold
ct_prob - Static variable in class bacnet.utils.UNAfold
CUFSL - Class in bacnet.scripts.listeriomics.technology
CUFSL() - Constructor for class bacnet.scripts.listeriomics.technology.CUFSL
CURATED - Enum constant in enum org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
CURATEDARRAY_CURATED - Static variable in class bacnet.datamodel.proteomics.NTermCreateData: List of column names for the final curated table of mapping
curateGenomeFindingDoublonGeneName(GenomeNCBI) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools: Check if two different locustag are not associated to the same GeneName
curateMatrix(String, boolean) - Static method in class bacnet.scripts.arrayexpress.ArrayExpress: Read a potential ExpressionMatrix, remove all duplicate rows by calculating mean when 2 or more rows have same name.
curateMatrix(String, boolean) - Static method in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressListeriomics: Read a potential ExpressionMatrix, remove all duplicate rows by calculating mean when 2 or more rows have same name.
curateMatrix(String, boolean) - Static method in class bacnet.scripts.listeriomics.ArrayExpressListeriomics: Read a potential ExpressionMatrix, remove all duplicate rows by calculating mean when 2 or more rows have same name.
curateRawData(String, String) - Static method in class bacnet.scripts.listeriomics.technology.IHM: Raw data from E-GEOD-12151 are not well formatted, not Tab delimited, so we need to extacrt a proper table from it, before working on it
curateRawData(String, String) - Static method in class bacnet.scripts.listeriomics.technology.UGiessen: Delete all first 4 columns of each raw data
curateTechnoTable(String) - Static method in class bacnet.scripts.listeriomics.technology.Febit: In some column Gene locus name is missing so we add it using EGDe genome and GenBank ID of each gene
CUTOFF - Static variable in class bacnet.raprcp.NavigationManagement
CUTOFF_EVALUE - Static variable in class bacnet.scripts.blast.BlastResult
CUTOFF_INTENSITIES - Static variable in class bacnet.scripts.blast.BlastResult
CW - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
CYAN - Static variable in class bacnet.utils.BasicColor

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