Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- A(double, double) - Static method in class bacnet.scripts.core.stat.AMtools
-
Calculate A = (x1+x2)/2
Represents mean value of x1+x2 - A_nk(int, int) - Static method in class bacnet.utils.MathUtils
-
Calculate the argument A_nk
- absoluteTOrelativeValue() - Method in class bacnet.genomeBrowser.core.DataTrack
-
Changed all BioCondition to display when switching from "ABSOLUTE VALUE DISPLAY3 to "RELATIVE VALUE DISPLAY"
- AbstractCompound - Class in org.biojava3.core.sequence.template
-
The details of a Compound
- AbstractCompound(String) - Constructor for class org.biojava3.core.sequence.template.AbstractCompound
- AbstractCompoundSet<C extends Compound> - Class in org.biojava3.core.sequence.template
- AbstractCompoundSet() - Constructor for class org.biojava3.core.sequence.template.AbstractCompoundSet
- AbstractCompoundTranslator<F extends Compound,
T extends Compound> - Class in org.biojava3.core.sequence.template - AbstractCompoundTranslator(SequenceCreatorInterface<T>, CompoundSet<F>, CompoundSet<T>) - Constructor for class org.biojava3.core.sequence.template.AbstractCompoundTranslator
- AbstractEdit(int) - Constructor for class org.biojava3.core.sequence.edits.Edit.AbstractEdit
- AbstractEdit(int, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.AbstractEdit
- AbstractFeature<S extends AbstractSequence<C>,
C extends Compound> - Class in org.biojava3.core.sequence.features -
A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
- AbstractFeature(String, String) - Constructor for class org.biojava3.core.sequence.features.AbstractFeature
-
A feature has a type and a source
- AbstractLocation - Class in org.biojava3.core.sequence.location.template
-
Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand
- AbstractLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.template.AbstractLocation
-
Default constructor
- AbstractLocation(Point, Point, Strand, boolean, boolean, AccessionID, List<Location>) - Constructor for class org.biojava3.core.sequence.location.template.AbstractLocation
-
Default constructor
- AbstractNucleotideCompoundSet<C extends NucleotideCompound> - Class in org.biojava3.core.sequence.template
- AbstractNucleotideCompoundSet() - Constructor for class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
- AbstractSequence<C extends Compound> - Class in org.biojava3.core.sequence.template
-
The base class for DNA, RNA and Protein sequences.
- AbstractSequence() - Constructor for class org.biojava3.core.sequence.template.AbstractSequence
- AbstractSequence(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.template.AbstractSequence
-
Create a Sequence from a simple string where the values should be found in compoundSet
- AbstractSequence(SequenceReader<C>, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.template.AbstractSequence
-
A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.
- AbstractSequence.AnnotationType - Enum in org.biojava3.core.sequence.template
- AccesionedLocation - Interface in org.biojava3.core.sequence.location.template
-
A location which is bound to an AccessionID.
- Accessioned - Interface in org.biojava3.core.sequence.template
-
Indicates an entity is accessioned
- AccessionID - Class in org.biojava3.core.sequence
-
Used in Sequences as the unique indentifier.
- AccessionID() - Constructor for class org.biojava3.core.sequence.AccessionID
- AccessionID(String) - Constructor for class org.biojava3.core.sequence.AccessionID
- AccessionID(String, DataSource) - Constructor for class org.biojava3.core.sequence.AccessionID
- AcD3 - Enum constant in enum bacnet.datamodel.proteomics.NTerm.TypeModif
- Ace - Enum constant in enum bacnet.datamodel.proteomics.NTerm.TypeModif
- aCM - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
- Activator - Class in bacnet.e4.rap.setup
-
OSGI Activator of bacnet.e4.rap.setup
- Activator - Class in bacnet.scripts
-
OSGI Activator of bacnet.scripts
- Activator() - Constructor for class bacnet.e4.rap.setup.Activator
- Activator() - Constructor for class bacnet.scripts.Activator
- add(String) - Method in class bacnet.utils.StringColor
-
Add text Default colorization will be applied BLACK = Foreground WHITE = Background
- add(String, Color, Color) - Method in class bacnet.utils.StringColor
-
Add text colorF will be applied to the foreground colorB will be applied to the background
- add(Collection<FeatureI>) - Method in class org.biojava3.genome.parsers.gff.FeatureList
-
Add all features in the specified list or collection to this list.
- add(FeatureI) - Method in class org.biojava3.genome.parsers.gff.FeatureList
-
Add specified feature to the end of the list.
- addAlignedSequence(S) - Method in class org.biojava3.core.sequence.MultipleSequenceAlignment
-
A sequence that has been aligned to other sequences will have inserts.
- addAnnotation(ExpressionMatrix, Genome) - Static method in class bacnet.datamodel.annotation.Annotation
-
Add annotation information to an ExpressionMatrix
- addAnnotationFromGFF(File, LinkedHashMap<String, ChromosomeBacteriaSequence>) - Static method in class bacnet.reader.GFFNCBIReader
-
Read a GFF and for each Gene associate all the corresponding information
- addAnnotationLite(ExpressionMatrix, Genome) - Static method in class bacnet.datamodel.annotation.Annotation
-
Add annotation information to an ExpressionMatrix
- addAnnotationMultiChromosome(ExpressionMatrix, Genome) - Static method in class bacnet.datamodel.annotation.Annotation
-
Add annotation information to an ExpressionMatrix
- addB(String, Color) - Method in class bacnet.utils.StringColor
-
Add text The colorization will be applied on the BACKGROUND
- addBioCond(BioCondition) - Method in class bacnet.datamodel.expdesign.Experiment
-
Add using the bioCondName as a key
- addBioCond(String, BioCondition) - Method in class bacnet.datamodel.expdesign.Experiment
-
Add using a specific Key
- addBioCondition(String) - Method in class bacnet.genomeBrowser.core.DataTrack
-
Read every ExpressionData contained in bioCondName
- addCDS(AccessionID, int, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
-
Add a Coding Sequence region with phase to the transcript sequence
- addChildElement(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
- addCodingRegionFeaturesFromFFN(File, File, LinkedHashMap<String, ChromosomeBacteriaSequence>) - Static method in class bacnet.reader.FastaFileReader
-
From a .ffn file in root/file.faa We had all CodingInfo into the ChromosomeSequence This method use my personal NCBIFastaHeaderParser
- addColumn(double[][], double[]) - Static method in class bacnet.utils.ArrayUtils
- addColumn(String[][], String[]) - Static method in class bacnet.utils.ArrayUtils
- addColumn(String, double[]) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
-
Add a column at the end of Matrix
- addComparisonFromTable(String) - Static method in class bacnet.scripts.database.BioConditionCreation
-
Read a Table and construct the list of Comparisons from it
- addComparisonFromTable(ArrayList<String>, String) - Static method in class bacnet.scripts.database.BioConditionCreation
-
Read a Table and construct the list of Comparisons from it
- addDeviation(ExpressionMatrix, ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
- addEGDeFilter() - Static method in class bacnet.scripts.listeriomics.nterm.RASToverlap
-
Read "10403S-noMatch-overlap.txt" and add a column indicating if the corresponding lmo gene is kept or not in "EGD-e-noMatch-decision.txt"
- addElement(NTerm) - Method in class bacnet.datamodel.dataset.NTermData
-
Add a NTerm in elements HashMap:
key = nTerm.getName()
value = nTerm - addElement(Object[], String) - Static method in class bacnet.utils.VectorUtils
-
Add an element to the end of the vector
- addElement(Color[], Color) - Method in class bacnet.utils.StringColor
- addExon(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
-
Add an ExonSequence mainly used to mark as a feature
- addExperimentFromTable(String) - Static method in class bacnet.scripts.database.BioConditionCreation
-
Read a Table summarizing all BioCondition and parse every information available
Save in BioCondition.PATH everyBioConditioncreated - addExperimentFromTable(String, ArrayList<String>, String) - Static method in class bacnet.scripts.database.BioConditionCreation
-
Read a Table summarizing all BioCondition and parse every information available
Save in BioCondition.PATH everyBioConditioncreated - addF(String, Color) - Method in class bacnet.utils.StringColor
-
Add text The colorization will be applied on the FOREGROUND
- addFeature(int, int, FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
-
Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
- addFeature(FeatureInterface<AbstractSequence<C>, C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
-
Add a feature to this sequence.
- addGene(AccessionID, int, int, Strand) - Method in class org.biojava3.core.sequence.ChromosomeSequence
-
Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
- addGeneFeaturesFromPTT(File, File, LinkedHashMap<String, ChromosomeBacteriaSequence>) - Static method in class bacnet.reader.PTTReader
-
Add feature from a PTT file
IMPORTANT: Need to be modified! - addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
-
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
- addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
- addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
- addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava3.genome.GeneFeatureHelper
-
Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete
- addHeader(String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
- addHomologToGene(String) - Static method in class bacnet.scripts.database.HomologCreation
-
Add homologs to every gene by parsing all homolog tables
- addInfoTOGenomePhylogeny(Phylogeny) - Static method in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
-
Get a Phylogeny where nodeName contain ID from Jolley and add all taxonomy information contained in it
- addInfoToPhylogeny(Phylogeny, HashMap<String, String[]>) - Static method in class bacnet.scripts.phylogeny.PhylogenyTools
- addInfoToPhylogeny(Phylogeny, HashMap<String, String[]>) - Static method in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
- addIntron(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
-
Add an Intron Currently used to mark an IntronSequence as a feature
- addIntronsUsingExons() - Method in class org.biojava3.core.sequence.GeneSequence
-
Once everything has been added to the gene sequence where you might have added exon sequences only then you can infer the intron sequences and add them.
- addition(double, double[][], double, double[][]) - Static method in class bacnet.utils.ArrayUtils
-
return=(coeff1)*array1 + (coeff2)*array2
- addition(double, double[], double, double[]) - Static method in class bacnet.utils.VectorUtils
-
return=(coeff1)*array1 + (coeff2)*array2
- addition(ExpressionMatrix, ExpressionMatrix, boolean) - Static method in class bacnet.utils.ExpressionMatrixStat
-
Perform an addition or soustraction between two ExpressionMatrix
First the intersection in term of RowNames and headers is found, then addition is done for each row - addLocusChange() - Static method in class bacnet.datamodel.annotation.LocusTag
- addMaXQuantInfo(NTermData, String) - Static method in class bacnet.datamodel.proteomics.NTermCreateData
-
Compare to peptides from MaxQuant software analysis
For each NTerm search if the same peptide and the same modif has been found in MaxQuant analysis. - addMaXQuantInfo(NTermData, String, boolean) - Static method in class bacnet.datamodel.proteomics.NTermCreateData
-
Add MaxQuant information for each peptide
This function is used only when multiple files are available - addMaXQuantInfo(NTermData, String, int) - Static method in class bacnet.datamodel.proteomics.NTermCreateData
- addMean(ExpressionMatrix, ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
- addMedian(ExpressionMatrix, ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
- addMissingValuesToMatrices(Experiment, Genome) - Static method in class bacnet.scripts.database.ProteomicsCreation
-
In order to represent proteomics data we need to add a -1 value in every missing row.
ATTENTION: -1 is now a value when there is no value but it is detected - addNonCodingRegionFeaturesFromFRN(File, File, LinkedHashMap<String, ChromosomeBacteriaSequence>) - Static method in class bacnet.reader.FastaFileReader
-
From a .frn file in root/file.frn We add all Noncoding Info into the ChromosomeSequence This method use my personal NCBIFastaHeaderParser
- addNote(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
-
Add notes about this sequence that will get exported for GFF3
- addPages() - Method in class bacnet.table.gui.ColorMapperWizard
- addPhylogenyToGenes() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics
-
Go through all result files and create Conservation HadhMap for each Gene
- addProperty(String, String) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
-
Add a property and type to associate with this DBReferenceInfo
- addProteomesToDatabase(ArrayList<String>) - Static method in class bacnet.scripts.database.ProteomicsCreation
-
Clean proteomics tables, and convert them for the database
- AddProteomicsDataDialog - Class in bacnet.genomeBrowser.dialog
- AddProteomicsDataDialog(Shell, Track) - Constructor for class bacnet.genomeBrowser.dialog.AddProteomicsDataDialog
-
Create the dialog.
- addQuantity(Number) - Method in class org.biojava3.core.sequence.features.QuantityFeature
- addRASTInfo() - Static method in class bacnet.scripts.listeriomics.nterm.NTermMain
-
Add RAST info to final supplementary tables
- addRow(double[][], double[]) - Static method in class bacnet.utils.ArrayUtils
- addRow(String[][], String[], int) - Static method in class bacnet.utils.ArrayUtils
-
Add the input row in the String[][] array, at the postiion given by index integer
- addRow(String, double[]) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
-
Add a row at the end of values
- addSet(String, ArrayList<String>) - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
- addStartCodonSequence(AccessionID, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
- addStopCodonSequence(AccessionID, int, int) - Method in class org.biojava3.core.sequence.TranscriptSequence
- addToCache(String, File) - Static method in class org.biojava3.core.util.FlatFileCache
- addToGenome(String) - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN
-
Add Srna to any Genome by reading BlastResults and extracting the lower e-value result
Srna with an identities less than 25% are not kept!!! - addTotalSpectraCount() - Static method in class bacnet.scripts.listeriomics.nterm.NTermMain
- addTranscript(AccessionID, int, int) - Method in class org.biojava3.core.sequence.GeneSequence
-
Add a transcription sequence to a gene which describes a ProteinSequence
- addTranscriptomeToDatabase(ArrayList<String>, String) - Static method in class bacnet.scripts.database.TranscriptomesCreation
-
Convert all transcriptomics files
- Convert all Seq data: RNASeq, RiboSeq, TSS, TermSeq
- Convert all GeneExpression and Tiling
- Convert all ExpressionMatrix - AddTranscriptomicsDataDialog - Class in bacnet.genomeBrowser.dialog
- AddTranscriptomicsDataDialog(Shell, Track) - Constructor for class bacnet.genomeBrowser.dialog.AddTranscriptomicsDataDialog
-
Create the dialog.
- addVariance(ExpressionMatrix, ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
- adfCleaning() - Static method in class bacnet.scripts.arrayexpress.ArrayExpressTechnology
- adjust(ExpressionMatrix, StatTest, boolean) - Static method in class bacnet.scripts.core.stat.FDR
- Agilent - Class in bacnet.scripts.listeriomics.technology
- Agilent() - Constructor for class bacnet.scripts.listeriomics.technology.Agilent
- alignblastN(String, String, String, double) - Static method in class bacnet.scripts.blast.Blast
-
Run a BlastN given a sequence name, an amino acid sequence and a database name
- alignBlastP(String, String, ArrayList<String>) - Static method in class bacnet.scripts.listeriomics.srna.SmallPeptidesSearch
-
Deprecated.
- alignLength - Variable in class bacnet.scripts.blast.BlastResult
- alignProtein(String, String, String, double) - Static method in class bacnet.scripts.blast.Blast
-
Run a BlastP given a sequence name, an amino acid sequence and a database name
- alignTblastN(String, String, String, double) - Static method in class bacnet.scripts.blast.Blast
-
Run a TBlastN given a sequence name, an amino acid sequence and a database name
- ALL_SEQUENCES - Enum constant in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceCollection
- ALLBACTERIA_NWK_1 - Static variable in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
- ALLBACTERIA_NWK_2 - Static variable in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
- ALLBACTERIA_XML - Static variable in class bacnet.scripts.phylogeny.PhylogenyTools
- ALLBACTERIA_XML_1 - Static variable in class bacnet.scripts.phylogeny.PhylogenyTools
- ALLBACTERIA_XML_2 - Static variable in class bacnet.scripts.phylogeny.PhylogenyTools
- allfileExt - Static variable in class bacnet.reader.FastaFileReader
- ALLFIRMICUTES_AVAILABLE - Static variable in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
- ALLFIRMICUTES_NWK - Static variable in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
- ALN - Enum constant in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat
- AM(double[][]) - Static method in class bacnet.scripts.core.stat.AMtools
-
Calculate AM matrix
- AM(ExpressionMatrix) - Static method in class bacnet.scripts.core.stat.AMtools
- AmbiguityDNACompoundSet - Class in org.biojava3.core.sequence.compound
- AmbiguityDNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet
- AmbiguityRNACompoundSet - Class in org.biojava3.core.sequence.compound
- AmbiguityRNACompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AmbiguityRNACompoundSet
- aminoacidCharge - Static variable in class bacnet.datamodel.sequence.Codon
- AminoAcidCompound - Class in org.biojava3.core.sequence.compound
-
Used to describe an Amino Acid.
- AminoAcidCompound(AminoAcidCompoundSet, String, String, String, Float) - Constructor for class org.biojava3.core.sequence.compound.AminoAcidCompound
- AminoAcidCompoundSet - Class in org.biojava3.core.sequence.compound
-
Set of proteinogenic amino acids.
- AminoAcidCompoundSet() - Constructor for class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
- aminoAcidsCompounds(CompoundSet<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
- AMtools - Class in bacnet.scripts.core.stat
- AMtools() - Constructor for class bacnet.scripts.core.stat.AMtools
- Annotation - Class in bacnet.datamodel.annotation
- Annotation() - Constructor for class bacnet.datamodel.annotation.Annotation
- Annotation(String[][]) - Constructor for class bacnet.datamodel.annotation.Annotation
- AnnotationView - Class in bacnet.sequenceTools
- AnnotationView() - Constructor for class bacnet.sequenceTools.AnnotationView
- ANTI_SD_SEQ - Static variable in class bacnet.datamodel.sequence.Sequence
-
Anti-SD sequence taken from Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures Jiong Ma, Allan Campbell, and Samuel Karlin J.
- App - Class in org.biojava3.genome
-
Hello world!
- App() - Constructor for class org.biojava3.genome.App
- applyCutOff(String, NTerm, Sequence, int[]) - Method in class bacnet.datamodel.proteomics.NTermFilter
-
Read a cutoff
Interprete each cutoff by returning true of false if the NTerm pass the condition
If the cutoff contain an "or": parse it in two separate cutoff
If the cutoff starts with an "!" - applyFilter() - Method in class bacnet.datamodel.proteomics.NTermFilter
-
Search for overlap with Gene, sRNAn, asRNA and ncRNA of each NTerm
- AppSpecificMethods - Class in bacnet.e4.rap
-
All the methods which are specific to a webpage
- AppSpecificMethods() - Constructor for class bacnet.e4.rap.AppSpecificMethods
- ArrayExpress - Class in bacnet.scripts.arrayexpress
-
Different methods to curate and parse the different data for Listeriomics website
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE - ArrayExpress() - Constructor for class bacnet.scripts.arrayexpress.ArrayExpress
- ARRAYEXPRESS_PATH - Static variable in class bacnet.scripts.arrayexpress.ArrayExpress
- ArrayExpressDataImport - Class in bacnet.scripts.arrayexpress
-
List of methods to download all ArrayExpress needed for Listeriomics website
- ArrayExpressDataImport() - Constructor for class bacnet.scripts.arrayexpress.ArrayExpressDataImport
- ArrayExpressDataUtils - Class in bacnet.scripts.arrayexpress
- ArrayExpressDataUtils - Class in bacnet.scripts.listeriomics.ArrayExpress
- ArrayExpressDataUtils() - Constructor for class bacnet.scripts.arrayexpress.ArrayExpressDataUtils
- ArrayExpressDataUtils() - Constructor for class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils
- ArrayExpressListeriomics - Class in bacnet.scripts.listeriomics.ArrayExpress
-
Different methods to curate and parse the different data for Listeriomics website
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE - ArrayExpressListeriomics - Class in bacnet.scripts.listeriomics
-
Different methods to curate and parse the different data for Listeriomics website
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE - ArrayExpressListeriomics() - Constructor for class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressListeriomics
- ArrayExpressListeriomics() - Constructor for class bacnet.scripts.listeriomics.ArrayExpressListeriomics
- ArrayExpressTechnology - Class in bacnet.scripts.arrayexpress
-
List of methods to determine the different technology used
- ArrayExpressTechnology - Class in bacnet.scripts.listeriomics.ArrayExpress
-
List of methods to determine the different technology used
- ArrayExpressTechnology() - Constructor for class bacnet.scripts.arrayexpress.ArrayExpressTechnology
- ArrayExpressTechnology() - Constructor for class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology
- ArrayListProxySequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.loader
- ArrayListProxySequenceReader() - Constructor for class org.biojava3.core.sequence.loader.ArrayListProxySequenceReader
- ArrayListSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage
-
Stores a Sequence as a collection of compounds in an ArrayList
- ArrayListSequenceReader() - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
- ArrayListSequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
- ArrayListSequenceReader(List<C>, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.ArrayListSequenceReader
- ARRAYSCORR - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
- arrayToExpressionMatrix(String[][], boolean) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
- arrayToExpressionMatrix(String[][], boolean, String) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
- arrayToExpressionMatrixList(String[][]) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
- ArrayUtils - Class in bacnet.utils
-
Public class with general array manipulation utilities, not specific to PROJECTNAME.
- ArrayUtils() - Constructor for class bacnet.utils.ArrayUtils
- ARROW_SIZE - Static variable in class bacnet.genomeBrowser.tracksGUI.GElement
-
Size of the arrow drawn in each rectangle to indicate strand
- ASN - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
- ASN_Bin - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
- ASN_TxT - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
- ASrna - Enum constant in enum bacnet.datamodel.sequence.Sequence.SeqType
- ASrna - Enum constant in enum bacnet.datamodel.sequence.Srna.TypeSrna
- attribute(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
- attribute(String, String) - Method in interface org.biojava3.core.util.XMLWriter
-
Add an un-qualified attribute to an element.
- attribute(String, String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
- attribute(String, String, String) - Method in interface org.biojava3.core.util.XMLWriter
-
Add an attribute to an element.
- attributes() - Method in class org.biojava3.genome.parsers.gff.Feature
-
Get the string of key/value attributes.
- attributeValues(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList
-
Create a collection of the unique values for the specified key.
- AUTO_BOTH - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
- AUTO_GENEXPR - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
- AUTO_TILING - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
- available() - Method in class org.biojava3.core.util.UncompressInputStream
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form