V-Index

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V

validateBioConditions(String) - Method in class bacnet.scripts.database.DataValidation: Validate every bioconditionsss by loading them
validateCoExprNetworks(String) - Method in class bacnet.scripts.database.DataValidation: Validate Transcriptomes data by looking if streamingdata files exists
validateComparisons(String) - Method in class bacnet.scripts.database.DataValidation: Validate every comparisons by loading them
validateGenomes(String) - Method in class bacnet.scripts.database.DataValidation: Validate every genomes by loading them
validateProteomics(String) - Method in class bacnet.scripts.database.DataValidation: Validate Transcriptomes data by looking if streamingdata files exists
validateRegion(int) - Method in class bacnet.genomeBrowser.core.Region: This method is run after a zoom or a moveHorizontally it move the region to be sure that x1>0 and x2<lastIndex
validateTranscriptomics(String) - Method in class bacnet.scripts.database.DataValidation: Validate Transcriptomes data by looking if streamingdata files exists
VALUE - Enum constant in enum bacnet.datamodel.dataset.OmicsData.ColNames
valueOf(String) - Static method in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.dataset.OmicsData.ColNames: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.dataset.OmicsData.TypeData: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.proteomics.NTerm.ExperimentName: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.proteomics.NTerm.MappingFrame: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.proteomics.NTerm.TypeModif: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.sequence.NcRNA.TypeNcRNA: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.sequence.Sequence.SeqType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.datamodel.sequence.Srna.TypeSrna: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.genomeBrowser.core.Track.DisplayType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.scripts.core.stat.StatTest.TypeStat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.table.core.ColorMapper.TypeMapper: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.table.core.ColorMapperRCP.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.table.core.Filter.TypeFilter: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bacnet.utils.Filter.TypeFilter: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.DataSource: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.DNASequence.DNAType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.Strand: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.template.AbstractSequence.AnnotationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biojava3.core.sequence.transcription.Frame: Returns the enum constant of this type with the specified name.
values() - Static method in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.dataset.OmicsData.ColNames: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.dataset.OmicsData.TypeData: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.proteomics.NTerm.ExperimentName: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.proteomics.NTerm.MappingFrame: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.proteomics.NTerm.TypeModif: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.sequence.NcRNA.TypeNcRNA: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.sequence.Sequence.SeqType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.datamodel.sequence.Srna.TypeSrna: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.genomeBrowser.core.Track.DisplayType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.scripts.core.stat.StatTest.TypeStat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.table.core.ColorMapper.TypeMapper: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.table.core.ColorMapperRCP.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.table.core.Filter.TypeFilter: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bacnet.utils.Filter.TypeFilter: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.DataSource: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.DNASequence.DNAType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.Strand: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.template.AbstractSequence.AnnotationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biojava3.core.sequence.transcription.Frame: Returns an array containing the constants of this enum type, in the order they are declared.
VARIABLE_SEQUENCES - Enum constant in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection
variance(double[]) - Static method in class bacnet.utils.VectorUtils: Calculate variance of a vector V(X)=mean(X^2)-(mean(X))^2
variance(ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
varianceNormalization(Experiment) - Static method in class bacnet.scripts.database.TranscriptomesCreation: Run some scripts to analyse the statistics of the transcriptomics data and performed VarianceNormalization:
It will reduce the total variance of each data to 1
For each column of the ExpressionMatrix, multiply each value by: Math.sqr(1/var(x))
So final variance of each column is equal to zero
VarianceNormalization - Class in bacnet.scripts.core.normalization: Variance normalization methods which will reduce the total variance of each data to 1
For each column of the ExpressionMatrix, multiply each value by: Math.sqr(1/var(x))
So final variance of each column is equal to zero
VarianceNormalization() - Constructor for class bacnet.scripts.core.normalization.VarianceNormalization
VectorUtils - Class in bacnet.utils: Vector are array with one dimension like : String[] or double[]
VectorUtils() - Constructor for class bacnet.utils.VectorUtils
VennDiagram - Class in bacnet.scripts.core.vennDiagram: Class for creating sets necessary in Venn diagrams
Providing a list of sets (through ArrayList) it will find intersections, unions and differences between all sets.
VennDiagram() - Constructor for class bacnet.scripts.core.vennDiagram.VennDiagram
VennDiagram(TreeMap<String, ArrayList<String>>) - Constructor for class bacnet.scripts.core.vennDiagram.VennDiagram
verifFilter() - Method in class bacnet.datamodel.proteomics.NTermFilter: Run some tests to check that filters has been well applied
verifyAll() - Static method in class bacnet.scripts.database.GenomesCreation: Load all Genomes created, and save a table with the different information contains in the genomes
verifyBlastResults(String) - Static method in class bacnet.scripts.database.HomologCreation: Check every if every blastP has been performed and extract first information by calcuating indentities metric of each blast
verifyCodonUsage() - Static method in class bacnet.datamodel.annotation.CodonUsage: To verify the codon prediction on EGD-e genome we look at all the genome and count the number of AAA, ATG and CCC codons
verifyDatabase() - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: Look at each genome folder and look at the size of each data
verifyDatabase(String) - Static method in class bacnet.scripts.blast.BlastDatabase: Look at each genome folder and look at the size of each data
verifyDatabase(String) - Static method in class bacnet.scripts.database.HomologCreation: Look at each genome folder and look at the size of each data
verifyGene(Gene, String[][], String[][]) - Static method in class bacnet.scripts.genome.SDProfile: For a given Gene calculate its SD binding energy, and compare to the value given by SDProfile data
verifyResults(String) - Static method in class bacnet.scripts.genome.SDProfile: For each Gene calculate the anti-SD energy and compare it to the values given by the SDProfile
verifySequence(Sequence<C>) - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
verifySequence(Sequence<C>) - Method in interface org.biojava3.core.sequence.template.CompoundSet
verifySequence(Sequence<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
verifyTISDB() - Static method in class bacnet.scripts.blast.ProteinTools: Verify TISDB peptides:
Each peptide might have a R at the end, or no R at all Every EGD-e gene should be in this database
verifyTISDB() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: Verify TISDB peptides:
Each peptide might have a R at the end, or no R at all Every EGD-e gene should be in this database

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