T-Index

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T

TabDelimitedTableReader - Class in bacnet.reader
TabDelimitedTableReader() - Constructor for class bacnet.reader.TabDelimitedTableReader
table(Integer) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder: Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by ID.
table(String) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder: Uses the static instance of IUPACParser to find instances of IUPACParser.IUPACTables by its String name
table(Table) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
Table - Interface in org.biojava3.core.sequence.transcription: Provides a way of separating us from the specific IUPACParser.IUPACTable even though this is the only implementing class for the interface.
TABLE - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
TABLE_COMMENT - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
TABLE_PATH - Static variable in class bacnet.scripts.arrayexpress.ArrayExpressTechnology
TABLE_PATH - Static variable in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology
Table.CaseInsensitiveTriplet - Class in org.biojava3.core.sequence.transcription: Class used to hold three nucleotides together and allow for equality to be assessed in a case insensitive manner.
Table.Codon - Class in org.biojava3.core.sequence.transcription: Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon.
TableCompositeHeatMap - Class in bacnet.expressionAtlas: The Composite in which is displayed the heatmap
TableCompositeHeatMap(Composite, int, String, boolean, EPartService, Shell) - Constructor for class bacnet.expressionAtlas.TableCompositeHeatMap: Create the composite.
TableFilter - Class in bacnet.table.gui
TableFilter() - Constructor for class bacnet.table.gui.TableFilter
tableGeneEGDe() - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: Get all lmos from EGD-e, and extract different information:
The Translation Iinitiation region here is always: -20bp ---- 60bp around start codon Start codon SD energy Structure energy ....
TableHTMLExport - Class in bacnet.utils
TableHTMLExport() - Constructor for class bacnet.utils.TableHTMLExport
TableSWTComposite - Class in bacnet.table
TableSWTComposite(Composite, int, Shell, EPartService) - Constructor for class bacnet.table.TableSWTComposite: Create the composite.
TableSWTView - Class in bacnet.table
TableSWTView() - Constructor for class bacnet.table.TableSWTView
TableViewerComparator - Class in bacnet.table.core
TableViewerComparator() - Constructor for class bacnet.table.core.TableViewerComparator
Tasmania - Class in bacnet.scripts.listeriomics.technology
Tasmania() - Constructor for class bacnet.scripts.listeriomics.technology.Tasmania
TaxonomyID - Class in org.biojava3.core.sequence: A sequence can be associated with a species or Taxonomy ID
TaxonomyID(String, DataSource) - Constructor for class org.biojava3.core.sequence.TaxonomyID
tblastN - Static variable in class bacnet.scripts.blast.Blast
terminator - Enum constant in enum bacnet.datamodel.sequence.Sequence.SeqType
TermSeq - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
TermSeq_ARRAY - Static variable in class bacnet.scripts.listeriomics.MainListeriomics
TermSeq_HEADERS - Static variable in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
test() - Static method in class bacnet.scripts.core.Expression: Test ShowExpression.showExpression();
test() - Static method in class bacnet.scripts.genome.SDProfile
Test - Class in bacnet.e4.rap.setup: All methods which will be executed before or after interface run
Test() - Constructor for class bacnet.e4.rap.setup.Test
testApplicationContext(EPartService) - Method in class bacnet.e4.rap.SessionControl
testApplicationContext(EPartService) - Method in class bacnet.e4.rap.setup.SessionControl
TestGenomeBrowser - Class in bacnet.genomeBrowser
TestGenomeBrowser() - Constructor for class bacnet.genomeBrowser.TestGenomeBrowser
TestGenomeBrowser(TracksComposite, Track) - Constructor for class bacnet.genomeBrowser.TestGenomeBrowser
testLPE() - Static method in class bacnet.scripts.core.stat.LPE
TestPart - Class in bacnet.e4.rap
TestPart() - Constructor for class bacnet.e4.rap.TestPart
text - Variable in class bacnet.table.gui.ColorMapperWizardPage
TextFeature<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.features: A implmentation of AbstractFeature
TextFeature(String, String, String, String) - Constructor for class org.biojava3.core.sequence.features.TextFeature
THREE - Enum constant in enum org.biojava3.core.sequence.transcription.Frame
Tiling - Class in bacnet.datamodel.dataset: Tiling array data from Listeria tiling chip ArrayExpress id : A-MEXP-1572 *
Tiling - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
Tiling() - Constructor for class bacnet.datamodel.dataset.Tiling
Tiling(String) - Constructor for class bacnet.datamodel.dataset.Tiling
TilingGeneExprDataBase - Class in bacnet.scripts.listeriomics
TilingGeneExprDataBase() - Constructor for class bacnet.scripts.listeriomics.TilingGeneExprDataBase
TIS - Class in bacnet.datamodel.proteomics: This class is used to regroup different Nterm.
TIS() - Constructor for class bacnet.datamodel.proteomics.TIS
toArray(String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Transform an ExpressionMatrix to a String[][]
toArray(String, boolean, boolean) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Transform an ExpressionMatrix to a String[][]
toArray(ArrayList<String[]>) - Static method in class bacnet.utils.ArrayUtils
toArrayList() - Method in class bacnet.datamodel.dataset.Network: Export to ArrayList to send to d3.js viewer
toArrayList(String, String, ArrayList<ExpressionMatrix>) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix: Export in an array a List of ExpressionMatrix All ExpressionMatrix from the list are supposed to have the same headers, and thus the same number of column The first column = the annotation of each ExpressionMatrix The second column = the RowNames of each ExpressionMatrix
toColor(Device) - Method in class bacnet.table.core.ColorSWT
toExpressionMatrix() - Method in class bacnet.datamodel.dataset.GeneExpression: Transform a GeneExpression into an ExpressionMatrix
toExpressionMatrix() - Method in class bacnet.datamodel.dataset.Tiling: Transform a Tiling into an ExpressionMatrix
toList(String[]) - Static method in class bacnet.utils.VectorUtils: Return a ArrayList representation of the input vector
toList(String[][]) - Static method in class bacnet.utils.ArrayUtils
toList(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: For the given Sequence this will return a List filled with the Compounds of that Sequence.
Tools() - Constructor for class org.biojava3.core.sequence.location.template.Location.Tools
TOP_LEFT - Static variable in class bacnet.swt.SWTResourceManager: Style constant for placing decorator image in top left corner of base image.
TOP_RIGHT - Static variable in class bacnet.swt.SWTResourceManager: Style constant for placing decorator image in top right corner of base image.
toString() - Method in class bacnet.datamodel.annotation.RfamElement
toString() - Method in class bacnet.datamodel.dataset.ExpressionData
toString() - Method in class bacnet.datamodel.proteomics.NTerm
toString() - Method in class bacnet.datamodel.sequence.Operon
toString() - Method in class bacnet.datamodel.sequence.Sequence: Print different
toString() - Method in class bacnet.genomeBrowser.core.Region
toString() - Method in class bacnet.genomeBrowser.core.Zoom
toString() - Method in class bacnet.scripts.blast.BlastResult
toString() - Method in class bacnet.table.core.Filter
toString() - Method in class bacnet.utils.Filter
toString() - Method in class org.biojava3.core.sequence.AccessionID
toString() - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
toString() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
toString() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
toString() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
toString() - Method in class org.biojava3.core.sequence.location.SimplePoint
toString() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
toString() - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: String representation of the MSA
toString() - Method in class org.biojava3.core.sequence.template.AbstractCompound
toString() - Method in class org.biojava3.core.sequence.template.AbstractSequence
toString() - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns a simple view of the alignment profile.
toString() - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
toString() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
toString() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
toString() - Method in class org.biojava3.core.util.CRC64Checksum: Returns a zero-padded 16 character wide string containing the current value of this checksum in uppercase hexadecimal format.
toString() - Method in class org.biojava3.genome.parsers.gff.Feature
toString() - Method in interface org.biojava3.genome.parsers.gff.FeatureI: A string representation of the feature.
toString() - Method in class org.biojava3.genome.parsers.gff.FeatureList: Return a string representation of all features in this list.
toString() - Method in class org.biojava3.genome.parsers.gff.Location: Return a string representation of location.
toString() - Method in class org.biojava3.genome.parsers.gff.LocIterator: Get string representation of iterator.
toString(int) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Get a string representation of the MSA with a fixed width
toString(int) - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns a formatted view of the alignment profile.
toString(String[]) - Static method in class bacnet.utils.VectorUtils: Return a String representation of the input vector Tab delimited
toString(String[][]) - Static method in class bacnet.utils.ArrayUtils
toString(ArrayList<String[]>) - Static method in class bacnet.utils.ArrayUtils
toString(ArrayList<String>, String) - Static method in class bacnet.utils.ListUtils: Return a String version of the list
toString(TreeSet<String>) - Static method in class bacnet.utils.VectorUtils: Return a String representation of the input TreeSet Tab delimited
toString(TreeSet<String>, String) - Static method in class bacnet.utils.ListUtils: Return a String version of the TreeSet
toString(LightweightProfile.StringFormat) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment: Support for different MSA formats
toString(LightweightProfile.StringFormat) - Method in interface org.biojava3.core.sequence.template.LightweightProfile: Returns a formatted view of the alignment profile.
toString(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Shortcut to SequenceMixin.toStringBuilder(org.biojava3.core.sequence.template.Sequence) which calls toString() on the resulting object.
toStringBuilder(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: For the given Sequence this will return a StringBuilder object filled with the results of Compound#toString().
toStringCodingInfo(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Display the info contain in a coding DNASequence
toStringGenes() - Method in class bacnet.datamodel.sequence.Operon: Return a list of all genes part of this Operon
toStringInfo() - Method in class bacnet.datamodel.sequence.Operon: Return a String containing a description of Operon properties
toStringMatrix(double[][]) - Static method in class bacnet.utils.ArrayUtils
toStringNonCodingInfo(DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Display info contain in a non coding DNASequence
toVector(double[][]) - Static method in class bacnet.utils.ArrayUtils: Transform to a Vector an array
Track - Class in bacnet.genomeBrowser.core
Track() - Constructor for class bacnet.genomeBrowser.core.Track
Track(Genome, String) - Constructor for class bacnet.genomeBrowser.core.Track: Set every parameter using genome and chromosome number
Track.DisplayType - Enum in bacnet.genomeBrowser.core
TrackCanvasData - Class in bacnet.genomeBrowser.tracksGUI: A TrackCanvasData is the Canvas in which will be displayed datasets
TrackCanvasData(Composite, int, Composite) - Constructor for class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
TrackCanvasGenome - Class in bacnet.genomeBrowser.tracksGUI: A TrackCanvasGenome is the Canvas in which will be displayed genome annotation
TrackCanvasGenome(Composite, int) - Constructor for class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome: Initiate a canvas genome to display genome annotation
trackChangedFlag - Variable in class bacnet.genomeBrowser.core.Track
TracksComposite - Class in bacnet.genomeBrowser.tracksGUI: In TracksComposite both TrackCanvasData and TrackCanvasGenome will be displayed.
TracksComposite(Composite, int, boolean, EPartService, Shell) - Constructor for class bacnet.genomeBrowser.tracksGUI.TracksComposite: Create the composite.
TranscriptionEngine - Class in org.biojava3.core.sequence.transcription: Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence.
TranscriptionEngine.Builder - Class in org.biojava3.core.sequence.transcription: This class is the way to create a TranslationEngine.
TranscriptomesCreation - Class in bacnet.scripts.database: List of methods to add the different transcriptomic datasetsto your multi-omics website
TranscriptomesCreation() - Constructor for class bacnet.scripts.database.TranscriptomesCreation
TranscriptomicsDataFilterComposite - Class in bacnet.expressionAtlas
TranscriptomicsDataFilterComposite(Composite, int, TranscriptomicsView) - Constructor for class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
TranscriptomicsView - Class in bacnet.expressionAtlas: View in which is displayed the table with all transcriptomics data available
TranscriptomicsView() - Constructor for class bacnet.expressionAtlas.TranscriptomicsView
TranscriptSequence - Class in org.biojava3.core.sequence: This is the sequence if you want to go from a gene sequence to a protein sequence.
TranscriptSequence(GeneSequence, int, int) - Constructor for class org.biojava3.core.sequence.TranscriptSequence
transform(double[][], int) - Static method in class bacnet.utils.ArrayUtils: Transform all value of this array, using MathUtils.transform
transform(double[], int) - Static method in class bacnet.utils.VectorUtils: Transform all value of this vector, using MathUtils.transform
transform(double, int) - Static method in class bacnet.utils.MathUtils: Transform a value, according to the type of transformation
type = 0 -> log2(value)
type = 1 -> 2^value
type = 2 -> log10(value)
transformData() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics: For each genome save a list of genes and their homologs
translate(F) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
translate(F) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
translate(Sequence<NucleotideCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine: Quick method to let you go from a CDS to a Peptide quickly.
translateGenomes(int) - Static method in class bacnet.scripts.blast.MultiSequenceTBlastNProtein: Read all fasta file from each genome and create a list of every possible small peptides
Extract from NTermDatabase.createTISDB()
translateGenomes(int, String) - Static method in class bacnet.scripts.blast.BlastDatabase: Read all fasta file from each genome and create a list of every possible small peptides
Extract from NTermDatabase.createTISDB()
translateMany(F) - Method in class org.biojava3.core.sequence.template.AbstractCompoundTranslator
translateMany(F) - Method in interface org.biojava3.core.sequence.template.CompoundTranslator
translateNCodons() - Method in class org.biojava3.core.sequence.transcription.RNAToAminoAcidTranslator: Indicates if we want to force exact translation of compounds or not i.e. those with internal N RNA bases.
translateNCodons(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
TranslationException - Exception in org.biojava3.core.exceptions: Thrown from AbstractCompundTranslator
TranslationException(Exception) - Constructor for exception org.biojava3.core.exceptions.TranslationException
TranslationException(String) - Constructor for exception org.biojava3.core.exceptions.TranslationException
TranslationException(String, Exception) - Constructor for exception org.biojava3.core.exceptions.TranslationException
transpose() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
transpose(double[][]) - Static method in class bacnet.utils.ArrayUtils: Return transposed array of input
transpose(String[][]) - Static method in class bacnet.utils.ArrayUtils
trimStop(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
tRNA - Enum constant in enum bacnet.datamodel.sequence.NcRNA.TypeNcRNA
Trypsin_Actino_Insoluble - Enum constant in enum bacnet.datamodel.proteomics.NTerm.ExperimentName
Trypsin_Actino_Soluble - Enum constant in enum bacnet.datamodel.proteomics.NTerm.ExperimentName
Trypsin_Insoluble - Enum constant in enum bacnet.datamodel.proteomics.NTerm.ExperimentName
Trypsin_Soluble - Enum constant in enum bacnet.datamodel.proteomics.NTerm.ExperimentName
TSS - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
TSS_ARRAY - Static variable in class bacnet.scripts.listeriomics.MainListeriomics
TSS_HEADERS - Static variable in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
TSS_Innocua_HEADERS - Static variable in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
TSSNTermRiboSeqListeriomics - Class in bacnet.scripts.listeriomics: List of methods to process TSS, TermSeq, and RiboSeq of Listeriomics Some TSS and NTerm lists were provided in tab-delimited format.
TSSNTermRiboSeqListeriomics() - Constructor for class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
TSTUDENT - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
TSTUDENTTILING - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
TWO - Enum constant in enum org.biojava3.core.sequence.transcription.Frame
TwoBitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitArrayWorker(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker
TwoBitSequenceReader<C extends NucleotideCompound> - Class in org.biojava3.core.sequence.storage: Implementation of the 2bit encoding.
TwoBitSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
TwoBitSequenceReader(String, CompoundSet<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
TwoBitSequenceReader(TwoBitSequenceReader.TwoBitArrayWorker<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
TwoBitSequenceReader(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.TwoBitSequenceReader
TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound> - Class in org.biojava3.core.sequence.storage: Extension of the BitArrayWorker which provides the 2bit implementation code.
type() - Method in class org.biojava3.genome.parsers.gff.Feature: Get feature type, such as "exon" or "CDS".
type() - Method in interface org.biojava3.genome.parsers.gff.FeatureI: Get the feature type, for example, "exon", "CDS", etc.
TYPE_OVERLAPS - Static variable in class bacnet.datamodel.dataset.NTermData
TYPE_REPRESENTATION - Static variable in class bacnet.table.core.Filter
TYPE_REPRESENTATION - Static variable in class bacnet.utils.Filter

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