S-Index

A B C D E F G H I J L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

S

sameEnd(DNASequence, DNASequence, int) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Determine that to gene have the same end if their ending piosition are the same +- scale bp
save() - Method in class bacnet.datamodel.dataset.ExpressionData: Save stat and values in two separate files
Saving is done via DataStream to allow streaming reading
save() - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Serialize the vector of lines with an ObjectOutputStream.
save() - Method in class bacnet.datamodel.dataset.NTermData: Save in: TranscriptomeData.PATH_STREAMING + this.getName() + TranscriptomeData.EXTENSION Serialize the vector of lines with an ObjectOutputStream.
save(boolean) - Method in class bacnet.datamodel.dataset.NGS: Save stat and values in two separate files
Saving is done via DataStream to allow streaming reading
save(Object[][], String) - Static method in class bacnet.reader.TabDelimitedTableReader
save(Object[][], String, boolean, boolean) - Static method in class bacnet.reader.TabDelimitedTableReader: Save the array to the destination file parameter
save(String) - Method in class bacnet.datamodel.annotation.Annotation: Serialize the vector of lines with an ObjectOutputStream.
save(String) - Method in class bacnet.datamodel.annotation.Signature: Serialize the vector of lines with an ObjectOutputStream.
save(String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Serialize the vector of lines with an ObjectOutputStream.
save(String) - Method in class bacnet.datamodel.dataset.Network: Save stat and values in two separate files
Saving is done via DataStream to allow streaming reading
save(String) - Method in class bacnet.datamodel.expdesign.BioCondition: Prompt the user for a filename, and save the scribble in that file.
save(String) - Method in class bacnet.datamodel.expdesign.Experiment: Prompt the user for a filename, and save the scribble in that file.
save(String) - Method in class bacnet.datamodel.sequence.Sequence: Serialize the vector of lines with an ObjectOutputStream.
save(String) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas: Serialize the vector of lines with an ObjectOutputStream.
save(String) - Method in class bacnet.genomeBrowser.core.Track
save(String) - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
save(String) - Method in class bacnet.table.core.ColorMapper
save(String) - Method in class bacnet.table.core.ColorMapperRCP
save(String) - Method in class bacnet.table.core.Filter: Prompt the user for a filename, and save the scribble in that file.
save(String) - Method in class bacnet.utils.Filter: Prompt the user for a filename, and save the scribble in that file.
saveCDS(ArrayList<Gene>, String) - Static method in class bacnet.reader.FastaFileReader: Save all amino acid sequence in a fasta file
saveFile(String, File, String, EPartService, Shell) - Static method in class bacnet.raprcp.SaveFileUtils: Same as saveTextFile but with no Preview
SaveFileUtils - Class in bacnet.raprcp: Utils methods for managinf files.
SaveFileUtils() - Constructor for class bacnet.raprcp.SaveFileUtils
saveHashMap(HashMap<String, String>, String) - Static method in class bacnet.reader.TabDelimitedTableReader: Save HashMap<String, String> to a 2 columns tab-delimited table
saveInHTML(Object[][], String, String) - Static method in class bacnet.reader.TabDelimitedTableReader: Save the table in a text file containing an HTML table
saveList(ArrayList<String>, String) - Static method in class bacnet.reader.TabDelimitedTableReader: Save an ArrayList of String in a tabdelimited table
saveLocusTagToOldLocusTag() - Method in class bacnet.datamodel.sequence.Genome: Save locusTagToOldLocusTag in a file for HomologCreation
saveProteinIdToLocusTag() - Method in class bacnet.datamodel.sequence.Genome: Save proteinIdnToLocusTag in a file for HomologCreation
saveProteinIdToOldLocusTag() - Method in class bacnet.datamodel.sequence.Genome: Save locusTagToOldLocusTag in a file for HomologCreation
saveProteins(ArrayList<Gene>, String) - Static method in class bacnet.reader.FastaFileReader: Save all amino acid sequence in a fasta file
saveProteins(ArrayList<Gene>, String, Chromosome) - Static method in class bacnet.reader.PTTReader: Save list of Gene in a PTT file
Information about the resulting protein are written into different columns:
"Location","Strand","Length","PID","Gene","Synonym","Code","COG","Product"
saveProteolyses(ArrayList<TIS>, String) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStatProteolyse: Save list of protoelyses hashmap
saveTab(String, String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Save in a TabDelimited text file
saveText(String) - Method in class bacnet.datamodel.annotation.Signature: Save Signature in a readable text file
saveText(String, String) - Static method in class bacnet.utils.FileUtils
saveText(String, String, boolean, boolean) - Static method in class bacnet.utils.FileUtils: Save text from "text" into fileName
saveTextFile(String, String, boolean, String, String, EPartService, Shell) - Static method in class bacnet.raprcp.SaveFileUtils: Save a text file
saveToFileList(String, String, String, ArrayList<ExpressionMatrix>) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
saveToFileList(String, String, String, ArrayList<ExpressionMatrix>, boolean, boolean) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
savetoTextFile() - Method in class bacnet.genomeBrowser.core.Track: Save Track information to a text file
saveTreeSet(TreeSet<String>, String) - Static method in class bacnet.reader.TabDelimitedTableReader: Save a TreeSet of String in a Tabdelimited table
SCATTER - Static variable in class bacnet.utils.HTMLUtils
SCATTER_NAME - Static variable in class bacnet.expressionAtlas.HeatMapMultiOmicsView
score() - Method in class org.biojava3.genome.parsers.gff.Feature: Get score.
SCRIPT_PATH - Variable in class bacnet.views.CRISPRPredictView
SCRIPT_PATH - Variable in class bacnet.views.CRISPRPredictView2
SCRIPT_SERVER - Variable in class bacnet.views.CRISPRPredictView
SD_ENERGY_CUTOFF - Static variable in class bacnet.scripts.genome.StartCodonProfile
SDProfile - Class in bacnet.scripts.genome: Calculate Shine-Dalgarno profile for bacterial genome.
SDProfile() - Constructor for class bacnet.scripts.genome.SDProfile
search(String) - Method in class bacnet.e4.rap.SynTView: Search a text file in the annotation
Search if it is a position and go Search if it is contains in getChromosome().getAllElements().keySet() Search if it is contains in gene.getName()
All the search are case insensitive using text.toUpperCase();
search(String) - Method in class bacnet.genomeBrowser.core.Track: Search a text file in the annotation
Search if it is a position and go Search if it is contains in getChromosome().getAllElements().keySet() Search if it is contains in gene.getName()
All the search are case insensitive using text.toUpperCase();
search(String) - Method in class bacnet.genomeBrowser.TestGenomeBrowser
search(String) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite: Search a specific element and center the view on it
search(String) - Method in class bacnet.sequenceTools.GeneView: Search a text file in the annotation
Search if it is a position and go Search if it is contains in getChromosome().getAllElements().keySet() Search if it is contains in gene.getName()
All the search are case insensitive using text.toUpperCase();
search(String) - Method in class bacnet.sequenceTools.SrnaView: Search a text file in the annotation
Search if it is a position and go Search if it is contains in getChromosome().getAllElements().keySet() Search if it is contains in gene.getName()
All the search are case insensitive using text.toUpperCase();
search(String) - Method in class bacnet.views.CoExprNetworkView: Search a text file in the annotation
Search if it is a position and go Search if it is contains in getChromosome().getAllElements().keySet() Search if it is contains in gene.getName()
All the search are case insensitive using text.toUpperCase();
SEARCH - Static variable in class bacnet.raprcp.NavigationManagement
searchElement(String) - Method in class bacnet.datamodel.sequence.Genome: Search in locustag names, gene name, and newlocustag if a gene is present or not
searchElement(DNASequence, String) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Search an element in the Note part of a DNASequence
searchElement(DNASequence, String, String) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools: Search an element in the Note part of a DNASequence in a sectio of the note : Section = gene, CDS, etc...
searchForSTandCC() - Static method in class bacnet.scripts.database.GenomesCreation: Concatenate all genomes together and create a huge fasta file.
searchMissingLocus() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics: By going through all GFF available search for the corresponding locustag
searchNterm(String) - Method in class bacnet.genomeBrowser.core.Track: Search an NTerm among all MassSpecData
searchPosition(String, String) - Static method in class bacnet.utils.FileUtils: Given a query sequence, find its different occurences on a database sequence
searchStopCodon(Genome, int, boolean) - Static method in class bacnet.datamodel.proteomics.NTermUtils: Get the next stop codon in frame and dowstream to a bpPosition
SecondStructureRNADialog - Class in bacnet.sequenceTools
SecondStructureRNADialog(Shell, String) - Constructor for class bacnet.sequenceTools.SecondStructureRNADialog: Create the dialog.
SEED - Static variable in class org.biojava3.core.util.Hashcoder: An initial value for a hashCode, to which we add contributions from fields.
select(Viewer, Object, Object) - Method in class bacnet.table.gui.TableFilter
selectByAttribute(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a list of all features that include the specified attribute key.
selectByAttribute(String, String) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a list of all features that include the specified attribute key/value pair.
selectByGroup(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a list of all features that have the specified group id, as defined by the group() method of the features.
selectByType(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a list of all features that are of the specified type, as defined by the type() method of the features.
selectByUserData(String) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a list of all features that include the specified key in their userMap().
selectByUserData(String, Object) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a list of all features that include the specified key/value pair in their userMap().
selectElements(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
selectFirstResult(String) - Static method in class bacnet.scripts.core.UNAfold: Remove duplicates results, keep only first result
selectFirstResult(String) - Static method in class bacnet.utils.UNAfold: Remove duplicates results, keep only first result
selectFirstResult(String, int) - Static method in class bacnet.scripts.core.UNAfold: Remove duplicates results, keep only first result
selectFirstResult(String, int) - Static method in class bacnet.utils.UNAfold: Remove duplicates results, keep only first result
SelectGenomeElementDialog - Class in bacnet.expressionAtlas.core: Dialog which allow specific selection of genes, smallRNAs and cisRegs
SelectGenomeElementDialog(Shell, EPartService, TreeSet<String>, TreeSet<String>, Genome) - Constructor for class bacnet.expressionAtlas.core.SelectGenomeElementDialog: Create the wizard.
selectOverlapping(String, Location, boolean) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a list of all features that overlap the specified location on the specified sequence.
selectParentElement(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
selectSingleElement(Element, String) - Static method in class org.biojava3.core.util.XMLHelper
SEPARATOR - Static variable in class bacnet.datamodel.expdesign.BioCondition: BioConditoon separator for comparisons
equal to " vs "
seqArraySize(int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
seqfileExt - Static variable in class bacnet.reader.FastaFileReader
seqname() - Method in class org.biojava3.genome.parsers.gff.Feature: Get the sequence name.
seqname() - Method in interface org.biojava3.genome.parsers.gff.FeatureI: Get the sequence name.
Sequence - Class in bacnet.datamodel.sequence: Object for manipulating part of Sequence.
Main attributes are name, begin, end, strand, genome, and type

SeqType {Gene,NcRNA,Operon,Srna,ASrna,terminator,unknown}

for each Sequence we force the condition:
this.begin inf_to this.end
Sequence<C extends Compound> - Interface in org.biojava3.core.sequence.template: Main interface for defining a collection of Compounds and accessing them using biological indexes
Sequence() - Constructor for class bacnet.datamodel.sequence.Sequence
Sequence(String, int, int) - Constructor for class bacnet.datamodel.sequence.Sequence: Create a Sequence object
if(begin>end)
this.end = begin
this.begin = end
this.strand = '-'
Sequence(String, int, int, char) - Constructor for class bacnet.datamodel.sequence.Sequence: Create a Sequence with a specific name, from, to and strand
CAREFUL:
from < to ALWAYS
sense is given by strand
If to < from it will correct automatically the position and strand, to have from < to
Sequence.SeqType - Enum in bacnet.datamodel.sequence
SequenceAsStringHelper<C extends Compound> - Class in org.biojava3.core.sequence.storage: This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data.
SequenceAsStringHelper() - Constructor for class org.biojava3.core.sequence.storage.SequenceAsStringHelper
SequenceComparator - Class in org.biojava3.core.sequence: Used to sort sequences
SequenceComparator() - Constructor for class org.biojava3.core.sequence.SequenceComparator
SequenceCreatorInterface<C extends Compound> - Interface in org.biojava3.core.sequence.io.template
SequenceDisplayDialog - Class in bacnet.sequenceTools
SequenceDisplayDialog(Shell, EPartService, Genome, String, boolean, int, int, Strand) - Constructor for class bacnet.sequenceTools.SequenceDisplayDialog: Create the dialog.
sequenceEquality(Sequence<C>, Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: A case-sensitive manner of comparing two sequence objects together.
sequenceEqualityIgnoreCase(Sequence<C>, Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: A case-insensitive manner of comparing two sequence objects together.
SequenceFileProxyLoader<C extends Compound> - Class in org.biojava3.core.sequence.loader: This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence.
SequenceFileProxyLoader(File, SequenceParserInterface, long, int, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
SequenceIterator(Sequence<C>) - Constructor for class org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator
SequenceLengthError - Error in org.biojava3.core.exceptions: Currently not used
SequenceLengthError(String) - Constructor for error org.biojava3.core.exceptions.SequenceLengthError
SequenceLocation<S extends AbstractSequence<C>,C extends Compound> - Class in org.biojava3.core.sequence.location: A location in a sequence that keeps a reference to its parent sequence
SequenceLocation(int, int, S) - Constructor for class org.biojava3.core.sequence.location.SequenceLocation
SequenceMixin - Class in org.biojava3.core.sequence.template: Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way.
SequenceMixin() - Constructor for class org.biojava3.core.sequence.template.SequenceMixin
SequenceMixin.SequenceIterator<C extends Compound> - Class in org.biojava3.core.sequence.template: A basic sequence iterator which iterates over the given Sequence by biological index.
SequenceOptimizationHints - Class in org.biojava3.core.sequence: A static class that provides optimization hints for memory or performance handling of sequence data.
SequenceOptimizationHints() - Constructor for class org.biojava3.core.sequence.SequenceOptimizationHints
SequenceOptimizationHints.SequenceCollection - Enum in org.biojava3.core.sequence
SequenceOptimizationHints.SequenceUsage - Enum in org.biojava3.core.sequence
SequenceParserInterface - Interface in org.biojava3.core.sequence.io.template
SequenceProxyView<C extends Compound> - Class in org.biojava3.core.sequence.template
SequenceProxyView() - Constructor for class org.biojava3.core.sequence.template.SequenceProxyView
SequenceProxyView(Sequence<C>) - Constructor for class org.biojava3.core.sequence.template.SequenceProxyView
SequenceProxyView(Sequence<C>, Integer, Integer) - Constructor for class org.biojava3.core.sequence.template.SequenceProxyView: Main constructor for working with SequenceProxyViews
SequenceReader<C extends Compound> - Interface in org.biojava3.core.sequence.template
SequenceTools - Class in org.biojava3.core.util
SequenceTools() - Constructor for class org.biojava3.core.util.SequenceTools
SequenceView<C extends Compound> - Interface in org.biojava3.core.sequence.template
service(HttpServletRequest, HttpServletResponse) - Method in class bacnet.raprcp.DownloadServiceHandler
SessionControl - Class in bacnet.e4.rap
SessionControl - Class in bacnet.e4.rap.setup: General methods for session control of an eclipse.rap application
SessionControl() - Constructor for class bacnet.e4.rap.SessionControl
SessionControl() - Constructor for class bacnet.e4.rap.setup.SessionControl
setAccession(AccessionID) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setAlias(String) - Method in class bacnet.datamodel.annotation.RfamElement
setAllBioConditions(ArrayList<String>) - Method in class bacnet.Database
setAllButtons(ArrayList<Button>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setAllButtons(ArrayList<Button>) - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
setAllButtons(ArrayList<Button>) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setAllComparisonStreamData(ArrayList<String>) - Static method in class bacnet.scripts.database.ComparisonsCreation: For each Comparison calculates corresponding TranscriptomeData, and save it
setAllElements(LinkedHashMap<String, Sequence>) - Method in class bacnet.datamodel.sequence.Chromosome
setAllFonts(Font) - Method in class bacnet.table.core.ColorMapperRCPList
setAllFonts(Font) - Method in class bacnet.table.core.ColorMapperList
setAlreadyRead(boolean) - Method in class bacnet.datamodel.dataset.ExpressionData
setAnnotation(Annotation) - Method in class bacnet.datamodel.dataset.NTermData
setAnnotation(Annotation) - Method in class bacnet.datamodel.sequence.Chromosome
setAnnotation(Annotation) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setAnnotation(Annotation) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setAnnotation(String[][]) - Method in class bacnet.datamodel.annotation.Annotation
setAnnotationFont(GC) - Static method in class bacnet.genomeBrowser.tracksGUI.GElement: Set Font to : "Arial",9,SWT.BOLD
setAnnotations(String[][]) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setAnnotationType(AbstractSequence.AnnotationType) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setAnnotElementHeight(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setAnnotNumber(float) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setAnnotSeparationHeight(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setAnnotSeparationNumber(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setAntiComparisons(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setAntiSDBindingFreeEnergy(double) - Method in class bacnet.datamodel.proteomics.NTerm
setArray(String[][]) - Method in class bacnet.sequenceTools.SrnaSummaryView
setArrayDataList(String[][]) - Method in class bacnet.sequenceTools.GeneView
setArrayDataList(String[][]) - Method in class bacnet.sequenceTools.SrnaView
setArrayExpressArrayLink(String) - Static method in class bacnet.utils.RWTUtils
setArrayExpressExpLink(String) - Static method in class bacnet.utils.RWTUtils
setArrayExpressId(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setArrayExpressTechnoId(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setArrayGeneToLocalization(String[][]) - Method in class bacnet.sequenceTools.GeneView
setArrayListWithAnnotation(String) - Method in class bacnet.datamodel.sequence.Chromosome: Read Annotation and from the list of sequences obtained, create the different LinkedHashMap
This method is run at the construction of a Genome object
setArrayProteomeList(String[][]) - Method in class bacnet.sequenceTools.GeneView
setArrayTranscriptomesList(String[][]) - Method in class bacnet.sequenceTools.GeneView
setAsRNAListEGDe(ArrayList<String>) - Method in class bacnet.Database
setAsRNAs(ArrayList<Srna>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setAsRNAs(LinkedHashMap<String, Srna>) - Method in class bacnet.datamodel.sequence.Chromosome
setaTISCutoff(int) - Method in class bacnet.datamodel.proteomics.NTermFilter
setaTISMap(HashMap<String, ArrayList<NTerm>>) - Method in class bacnet.datamodel.dataset.NTermData
setBegin(int) - Method in class bacnet.datamodel.annotation.RfamElement
setBegin(int) - Method in class bacnet.datamodel.sequence.Sequence
setBegin(int) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setBioBegin(Integer) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setBioCondition() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
setBioConditionHashMaps(LinkedHashMap<String, BioCondition>) - Method in class bacnet.genomeBrowser.core.DataTrack
setBioconditions(HashMap<String, Boolean>) - Method in class bacnet.scripts.database.DataValidation
setBioConditions(ArrayList<BioCondition>) - Method in class bacnet.scripts.core.Expression
setBioConditions(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
setBioConditionsArrayPath(String) - Method in class bacnet.Database
setBioCondName(String) - Method in class bacnet.datamodel.dataset.OmicsData
setBioConds(ArrayList<String[]>) - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
setBioConds(ArrayList<String[]>) - Method in class bacnet.expressionAtlas.ProteomicsView
setBioConds(ArrayList<String[]>) - Method in class bacnet.expressionAtlas.TranscriptomicsView
setBioConds(ArrayList<String[]>) - Method in class bacnet.genomeBrowser.NTerminomicsView
setBioConds(ArrayList<String[]>) - Method in class bacnet.sequenceTools.AnnotationView
setBioConds(ArrayList<String[]>) - Method in class bacnet.sequenceTools.GeneView
setBioConds(LinkedHashMap<String, BioCondition>) - Method in class bacnet.datamodel.expdesign.Experiment
setBioCondsArray(String[][]) - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
setBioCondsArray(String[][]) - Method in class bacnet.expressionAtlas.ProteomicsView
setBioCondsArray(String[][]) - Method in class bacnet.expressionAtlas.TranscriptomicsView
setBioCondsArray(String[][]) - Method in class bacnet.genomeBrowser.NTerminomicsView
setBioCondsArray(String[][]) - Method in class bacnet.sequenceTools.AnnotationView
setBioCondsArray(String[][]) - Method in class bacnet.sequenceTools.GeneView
setBioCondsArray(String[][]) - Method in class bacnet.sequenceTools.GenomicsView
setBioCondsToDisplay(ArrayList<String[]>) - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
setBioCondsToDisplay(ArrayList<String[]>) - Method in class bacnet.expressionAtlas.ProteomicsView
setBioCondsToDisplay(ArrayList<String[]>) - Method in class bacnet.expressionAtlas.TranscriptomicsView
setBioCondsToDisplay(ArrayList<String[]>) - Method in class bacnet.genomeBrowser.NTerminomicsView
setBioCondsToDisplay(ArrayList<String[]>) - Method in class bacnet.sequenceTools.AnnotationView
setBioCondsToDisplay(ArrayList<String[]>) - Method in class bacnet.sequenceTools.GeneView
setBioCondsToDisplay(ArrayList<String[]>) - Method in class bacnet.sequenceTools.GenomicsView
setBioEnd(Integer) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setBioEnd(Integer) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
setBioStart(Integer) - Method in class org.biojava3.core.sequence.template.SequenceProxyView
setBlue(int) - Method in class bacnet.table.core.ColorSWT
setBpSizeH(double) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setBpSizeH(double) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setBtnAllMutant(Button) - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
setBtnAllMutant(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnChooseOneMutant(Button) - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
setBtnChooseOneMutant(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnDeath(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnDnDNA(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnDnProt(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnDnRNA(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnExponential(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnGeneExpression(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnLagPhase(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnNoDNA(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnNoneMutant(Button) - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
setBtnNoneMutant(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnNoProt(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnNoRNA(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnOpenStructure(Button) - Method in class bacnet.sequenceTools.SrnaView
setBtnPosDNA(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnPrint(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnRegrowth(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnRiboSeq(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnRnaseq(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnStationnary(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnSurvival(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnTermSeq(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnTiling(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnTss(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnUnpublished(Button) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setBtnUpdateCutoff(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnUpProt(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setBtnUpRNA(Button) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setCenterColor(Color) - Method in class bacnet.table.core.ColorMapper
setCenterColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setCenterColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setCenterColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setCenterPos(double) - Method in class bacnet.table.core.ColorMapper
setCenterPos(double) - Method in class bacnet.table.core.ColorMapperRCP
setCgview(Cgview) - Method in class bacnet.scripts.genome.CircularGenomeJPanel
setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in class org.biojava3.core.sequence.features.AbstractFeature: Set the children features
setChildrenFeatures(List<FeatureInterface<S, C>>) - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Set the children features
setChromoId(String) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setChromoID(String) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setChromosome(Chromosome) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setChromosome(Chromosome) - Method in class bacnet.genomeBrowser.core.Track
setChromosomeID(String) - Method in class bacnet.datamodel.annotation.Annotation
setChromosomeID(String) - Method in class bacnet.datamodel.dataset.ExpressionData
setChromosomeID(String) - Method in class bacnet.datamodel.sequence.Chromosome
setChromosomeID(String) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setChromosomeID(String) - Method in class bacnet.datamodel.sequence.Sequence
setChromosomeID(String) - Method in class bacnet.genomeBrowser.core.Track
setChromosomeNumber(int) - Method in class org.biojava3.core.sequence.ChromosomeSequence
setChromosomes(LinkedHashMap<String, Chromosome>) - Method in class bacnet.datamodel.sequence.Genome
setChromosomes(LinkedHashMap<String, ChromosomeBacteriaSequence>) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
setCisRegRNAListEGDe(ArrayList<String>) - Method in class bacnet.Database
setCisRegs(ArrayList<Srna>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setCisRegs(LinkedHashMap<String, Srna>) - Method in class bacnet.datamodel.sequence.Chromosome
setCmbChromo(Combo) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setCmbGenome(Combo) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setCodingSequenceHashMap(LinkedHashMap<String, DNASequence>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setCodonUsage(double) - Method in class bacnet.datamodel.proteomics.NTerm
setCoExprNetworkArrayPath(String) - Method in class bacnet.Database
setCoExprNetworks(HashMap<String, Boolean>) - Method in class bacnet.scripts.database.DataValidation
setCog(String) - Method in class bacnet.datamodel.sequence.Gene
setColorMapperList(ColorMapperList) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setColorMappers(TreeMap<ColorMapper.TypeMapper, ColorMapper>) - Method in class bacnet.table.core.ColorMapperList
setColorMappers(TreeMap<ColorMapperRCP.Type, ColorMapperRCP>) - Method in class bacnet.table.core.ColorMapperRCPList
setColorMapperValues(ArrayList<ExpressionMatrix>) - Static method in class bacnet.table.core.ColorMapper
setColorMapperValues(ArrayList<ExpressionMatrix>) - Static method in class bacnet.table.core.ColorMapperRCP
setColumn(int) - Method in class bacnet.table.core.BioConditionComparator
setColumn(int) - Method in class bacnet.table.core.TableViewerComparator
setColumnNames(ArrayList<String>) - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
setColumnNames(ArrayList<String>) - Method in class bacnet.expressionAtlas.ProteomicsView
setColumnNames(ArrayList<String>) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setColumnNames(ArrayList<String>) - Method in class bacnet.expressionAtlas.TranscriptomicsView
setColumnNames(ArrayList<String>) - Method in class bacnet.genomeBrowser.NTerminomicsView
setColumnNames(ArrayList<String>) - Method in class bacnet.sequenceTools.AnnotationView
setColumnNames(ArrayList<String>) - Method in class bacnet.sequenceTools.GenomicsView
setColumnNames(TreeSet<String>) - Method in class bacnet.table.core.ColorMapper
setColumnNames(TreeSet<String>) - Method in class bacnet.table.core.ColorMapperRCP
setComboAbsoluteRelative(Combo) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
setComboGenome(Combo) - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
setComboGenome(Combo) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setComboGenome(Combo) - Method in class bacnet.sequenceTools.GeneView
setComboMutant(Combo) - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
setComboMutant(Combo) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setComment(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setComment(String) - Method in class bacnet.datamodel.sequence.Sequence
setComparisons(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setComparisons(HashMap<String, Boolean>) - Method in class bacnet.scripts.database.DataValidation
setCompExpression(ExpressionMatrix) - Method in class bacnet.scripts.core.Comparison
setCompFilter(Composite) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setComposite(Composite) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setComposite_2(Composite) - Method in class bacnet.sequenceTools.SrnaView
setComposite_6(Composite) - Method in class bacnet.sequenceTools.SrnaView
setComposite_7(Composite) - Method in class bacnet.sequenceTools.SrnaView
setCompositeAddData(Composite) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
setCompositeDataFilter(ProteomicsDataFilterComposite) - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
setCompositeDataFilter(ProteomicsDataFilterComposite) - Method in class bacnet.expressionAtlas.ProteomicsView
setCompositeDataFilter(TranscriptomicsDataFilterComposite) - Method in class bacnet.expressionAtlas.TranscriptomicsView
setCompositeNterm(CompositeNTermInfo) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
setCompositeSummary(Composite) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setCompositeTypeDisplay(Composite) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
setCompoundAt(char, int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker: Converts from char to Compound and sets it at the given biological index
setCompoundAt(C, int) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker: Sets the compound at the specified biological index
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Class is immutable & so this is unsupported
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Unsupported
setCompoundSet(CompoundSet<C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setCompoundSet(CompoundSet<C>) - Method in interface org.biojava3.core.sequence.template.SequenceReader
setCompoundSet(CompoundSet<NucleotideCompound>) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
setConservation(int) - Method in class bacnet.datamodel.sequence.Sequence
setConservationHashMap(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.Sequence
setContainer(Composite) - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
setContents(String) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
setContents(String) - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
setContents(String) - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: Once the sequence is retrieved set the contents and make sure everything this is valid
setContents(String) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
setContents(String) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader: Class is immutable & so this is unsupported
setContents(String) - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
setContents(String) - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Unsupported
setContents(String) - Method in interface org.biojava3.core.sequence.template.SequenceReader
setContents(String) - Method in class org.biojava3.core.sequence.views.RnaSequenceView
setContents(List<C>) - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
setCurrentState(String) - Method in class bacnet.Database
setCutOff1(double) - Method in class bacnet.table.core.Filter
setCutOff1(double) - Method in class bacnet.utils.Filter
setCutOff2(double) - Method in class bacnet.table.core.Filter
setCutOff2(double) - Method in class bacnet.utils.Filter
setCutoffHashMap(HashMap<String, ArrayList<String>>) - Method in class bacnet.datamodel.proteomics.NTermFilter
setData(ExpressionMatrix, Genome) - Method in class bacnet.table.TableSWTView
setData(String, ArrayList<String>) - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView: set the Data for the genomeViewer
setDatabase(String) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
setDatabaseFeatures(HashMap<String, String>) - Method in class bacnet.Database
setDatabaseReferences(DatabaseReferenceInterface) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setDataColors() - Method in class bacnet.genomeBrowser.core.DataTrack: For each data assign a Color

OVERLAYBC : Color are always the same, blue and red for tiling, black for GeneExpr, other color for the rest
SUPERIMPOSED, OVERLAYDATA : Color.getColors(index) is used
setDataColors(TreeMap<String, Color>) - Method in class bacnet.genomeBrowser.core.DataTrack
setDataNameFont(GC) - Static method in class bacnet.genomeBrowser.tracksGUI.GElement: Set Font to : "Arial",11,SWT.BOLD
setDataNOTDisplayed(ArrayList<String>) - Method in class bacnet.genomeBrowser.core.DataTrack
setDataRead(boolean) - Method in class bacnet.datamodel.dataset.GeneExpression
setDataRegion(Region) - Method in class bacnet.genomeBrowser.core.Track
setDatas(DataTrack) - Method in class bacnet.genomeBrowser.core.Track
setDatasets(HashMap<String, ExpressionData>) - Method in class bacnet.datamodel.dataset.NGS
setDataSizes() - Method in class bacnet.genomeBrowser.core.DataTrack: For each data assign a Size

1.5 for Tiling array, GeneExpression array and RNASeq 1 for TSS 0.5 for NTerm and Proteomics data
setDataWindowSize(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setDate(String) - Method in class bacnet.datamodel.dataset.OmicsData
setDate(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setDecaySliderVBar(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setDefault() - Method in class bacnet.table.core.ColorMapper
setDefault() - Method in class bacnet.table.core.ColorMapperRCP
setDefault() - Method in class bacnet.table.core.Filter
setDefault() - Method in class bacnet.utils.Filter
setDefaultAlpha(GC) - Static method in class bacnet.genomeBrowser.tracksGUI.GElement: Set Alpha to 255
setDefaultColor() - Method in class bacnet.table.core.ColorMapper
setDefaultColor() - Method in class bacnet.table.core.ColorMapperRCP
setDefaultFont() - Method in class bacnet.table.core.ColorMapper
setDefaultFont(GC) - Static method in class bacnet.genomeBrowser.tracksGUI.GElement: Set Font to : "Arial",12,SWT.NORMAL
setDefaultPos() - Method in class bacnet.table.core.ColorMapper
setDefaultPos() - Method in class bacnet.table.core.ColorMapperRCP
setDescription(String) - Method in class bacnet.datamodel.annotation.Signature
setDescription(String) - Method in class org.biojava3.core.sequence.compound.CodonCompound
setDescription(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature
setDescription(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Set the description that can be used to describe the feature
setDescription(String) - Method in class org.biojava3.core.sequence.template.AbstractCompound
setDescription(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setDescription(String) - Method in interface org.biojava3.core.sequence.template.Compound
setDescription(String) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
setDescription(String) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
setDeviation(double) - Method in class bacnet.table.core.ColorMapper
setDeviation(double) - Method in class bacnet.table.core.ColorMapperRCP
setDisplay(boolean[]) - Method in class bacnet.genomeBrowser.core.DataTrack
setDisplay(Display) - Method in class bacnet.table.core.ColorMapper
setDisplayAbsoluteValue(boolean) - Method in class bacnet.genomeBrowser.core.DataTrack
setDisplayMouseLine(boolean) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setDisplayMouseLine(boolean) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setDisplayRegion(Region) - Method in class bacnet.genomeBrowser.core.Track
setDisplaySequence(boolean) - Method in class bacnet.genomeBrowser.core.Track
setDisplayType(Track.DisplayType) - Method in class bacnet.genomeBrowser.core.Track
setDNAType(DNASequence.DNAType) - Method in class org.biojava3.core.sequence.DNASequence
setDownDNAList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setDownloadLink(String) - Method in class bacnet.views.InternalBrowser
setDownProtList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setDownRNAList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setDuplicates(ArrayList<String>) - Method in class bacnet.datamodel.proteomics.NTerm
setDuplicateSequenceToRemove(ArrayList<String>) - Method in class bacnet.datamodel.proteomics.NTermFilter
setEdges(HashMap<String, HashMap<String, Double>>) - Method in class bacnet.datamodel.dataset.Network: An hashMap which map each vertex (=genome element) to the correlated vertex.
Vertex -> HashMap<Vetrex,PearsonCorrelation>
setElements(ArrayList<Sequence>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setElements(ArrayList<String>) - Method in class bacnet.datamodel.annotation.Signature
setElements(HashMap<String, NTerm>) - Method in class bacnet.datamodel.dataset.NTermData: Link NTerm name to NTerm
This correspond to the list of NTerm
setElements(LinkedHashMap<String, Sequence>) - Method in class bacnet.datamodel.sequence.Chromosome
setEnd(int) - Method in class bacnet.datamodel.annotation.RfamElement
setEnd(int) - Method in class bacnet.datamodel.sequence.Sequence
setEnd(int) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setExcludeColumn(ArrayList<String>) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setExcludeColumn(ArrayList<String>) - Method in class bacnet.table.core.Filter
setExcludeColumn(ArrayList<String>) - Method in class bacnet.table.core.FilterList
setExcludeColumn(ArrayList<String>) - Method in class bacnet.utils.Filter
setExcludeRow(ArrayList<String>) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setExcludeRow(ArrayList<String>) - Method in class bacnet.table.core.Filter
setExcludeRow(ArrayList<String>) - Method in class bacnet.table.core.FilterList
setExcludeRow(ArrayList<String>) - Method in class bacnet.utils.Filter
setExitConfirmation() - Static method in class bacnet.e4.rap.SessionControl
setExitConfirmation() - Static method in class bacnet.e4.rap.setup.SessionControl
setExperienceNb(int) - Method in class bacnet.datamodel.expdesign.BioCondition
setExperimentComparisonTablePath(String) - Method in class bacnet.Database
setExpression(ExpressionMatrix) - Method in class bacnet.scripts.core.Comparison
setExpression(ExpressionMatrix) - Method in class bacnet.scripts.core.Expression
setExpressionAlpha(GC) - Static method in class bacnet.genomeBrowser.tracksGUI.GElement: Set Alpha to 150
setExprProteomesTable(HashMap<String, ExpressionMatrix>) - Method in class bacnet.Database
setExprTranscriptomesTable(HashMap<String, ExpressionMatrix>) - Method in class bacnet.Database
setFeatures(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.Sequence
setFeaturesKeyWord(FeaturesKeyWordInterface) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setFile(File) - Method in class bacnet.raprcp.DownloadServiceHandler
setFileName(String) - Method in class bacnet.raprcp.DownloadServiceHandler
setFileName(String) - Method in class bacnet.views.InternalBrowser
setFilterColumn(boolean) - Method in class bacnet.table.core.Filter
setFilterColumn(boolean) - Method in class bacnet.utils.Filter
setFilteredNetwork(Network) - Method in class bacnet.e4.rap.SynTView
setFilteredNetwork(Network) - Method in class bacnet.views.CoExprNetworkView
setFilters(TreeMap<String, Filter>) - Method in class bacnet.table.core.FilterList
setFirstandSecondRowNameInList(ArrayList<ExpressionMatrix>, String, String) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
setFirstRowName(String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setFocus() - Method in class bacnet.e4.rap.setup.SetupPart
setFocus() - Method in class bacnet.e4.rap.TestPart
setFocus() - Method in class bacnet.views.CRISPRPredictView
setFocus() - Method in class bacnet.views.CRISPRPredictView2
setFocused(boolean) - Method in class bacnet.e4.rap.InitViewBacnet
setFocused(boolean) - Method in class bacnet.e4.rap.InitViewListeria
setFocused(boolean) - Method in class bacnet.e4.rap.InitViewListeriaSample
setFocused(boolean) - Method in class bacnet.e4.rap.InitViewYersinia
setFocused(boolean) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setFocused(boolean) - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
setFocused(boolean) - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
setFocused(boolean) - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
setFocused(boolean) - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
setFocused(boolean) - Method in class bacnet.expressionAtlas.ProteomicsView
setFocused(boolean) - Method in class bacnet.expressionAtlas.TranscriptomicsView
setFocused(boolean) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
setFocused(boolean) - Method in class bacnet.sequenceTools.AnnotationView
setFocused(boolean) - Method in class bacnet.sequenceTools.GeneView
setFocused(boolean) - Method in class bacnet.sequenceTools.GenomicsView
setFocused(boolean) - Method in class bacnet.sequenceTools.SrnaView
setFocused(boolean) - Method in class bacnet.views.CoExprNetworkView
setFontDouble(Font) - Method in class bacnet.table.core.ColorMapperRCP
setFontDouble(Font) - Method in class bacnet.table.core.ColorMapper
setFontRowName(Font) - Method in class bacnet.table.core.ColorMapper
setFontsDouble(Font) - Method in class bacnet.table.core.ColorMapperRCPList
setFontsDouble(Font) - Method in class bacnet.table.core.ColorMapperList
setFontsString(Font) - Method in class bacnet.table.core.ColorMapperRCPList
setFontsString(Font) - Method in class bacnet.table.core.ColorMapperList
setFontString(Font) - Method in class bacnet.table.core.ColorMapperRCP
setFontText(Font) - Method in class bacnet.table.core.ColorMapper
setFoundIn(ArrayList<String>) - Method in class bacnet.datamodel.sequence.Srna
setGeneExprs(ArrayList<GeneExpression>) - Method in class bacnet.datamodel.expdesign.BioCondition
setGeneListEGDe(ArrayList<String>) - Method in class bacnet.Database
setGeneModification(HashMap<String, ArrayList<NTerm.TypeModif>>) - Method in class bacnet.datamodel.dataset.NTermData
setGeneName(String) - Method in class bacnet.datamodel.sequence.Gene
setGeneNameToLocusTagMap(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.Chromosome
setGeneNameToLocusTagMap(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setGeneralExperiment(Experiment) - Method in class bacnet.Database
setGeneralNetwork(Network) - Method in class bacnet.e4.rap.SynTView
setGeneralNetwork(Network) - Method in class bacnet.views.CoExprNetworkView
setGenes(HashMap<String, ArrayList<NTerm>>) - Method in class bacnet.datamodel.dataset.NTermData
setGenes(LinkedHashMap<String, Gene>) - Method in class bacnet.datamodel.sequence.Chromosome
setGenes(TreeSet<String>) - Method in class bacnet.datamodel.sequence.Operon
setGenesAlternative(LinkedHashMap<String, Gene>) - Method in class bacnet.datamodel.sequence.Chromosome
setGeneSequence() - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: Create a fasta file with all the gene sequences
setGenome(Genome) - Method in class bacnet.scripts.core.Expression
setGenome(Genome) - Method in class bacnet.sequenceTools.AnnotationView
setGenome(Genome) - Method in class bacnet.sequenceTools.GeneView
setGenome(Genome) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setGenome(Genome) - Method in class bacnet.sequenceTools.SrnaView
setGenome(Genome) - Method in class bacnet.views.CoExprNetworkView
setGenome(String) - Method in class bacnet.datamodel.annotation.Annotation
setGenome(String) - Method in class bacnet.datamodel.annotation.Signature
setGenomeAA(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setGenomeAACompl(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setGenomeAAMinus(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setGenomeAAMinusCompl(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setGenomeAAPlus(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setGenomeAAPlusCompl(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setGenomeArrayPath(String) - Method in class bacnet.Database
setGenomeElements(ArrayList<String>) - Method in class bacnet.scripts.core.Comparison
setGenomeElements(ArrayList<String>) - Method in class bacnet.scripts.core.Expression
setGenomeList(ArrayList<String>) - Method in class bacnet.Database
setGenomeName(String) - Method in class bacnet.datamodel.dataset.ExpressionData
setGenomeName(String) - Method in class bacnet.datamodel.dataset.NGS
setGenomeName(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setGenomeName(String) - Method in class bacnet.datamodel.sequence.Sequence
setGenomeName(String) - Method in class bacnet.e4.rap.SynTView
setGenomeName(String) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setGenomeName(String) - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
setGenomeName(String) - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
setGenomeName(String) - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
setGenomeName(String) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setGenomeName(String) - Method in class bacnet.genomeBrowser.core.Track
setGenomeName(String) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setGenomeName(String) - Method in class bacnet.views.CoExprNetworkView
setGenomeNCBILink(String) - Static method in class bacnet.utils.RWTUtils
setGenomes(HashMap<String, Boolean>) - Method in class bacnet.scripts.database.DataValidation
setGenomes(TreeMap<String, Genome>) - Method in class bacnet.Database
setGenomeSelected(String) - Method in class bacnet.sequenceTools.GeneView: The comboGenome contains modified genome name so we need this method to select an element
a '*' is add to genome name when a transcriptome or proteome data is available
setGenomesNCBI(TreeMap<String, GenomeNCBI>) - Method in class bacnet.Database
setGenomeUsed(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setGoogleId(String) - Method in class bacnet.Database
setGreen(int) - Method in class bacnet.table.core.ColorSWT
setGrowth(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setHeader(String, int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setHeaderAnnotation(ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setHeaderColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setHeaderColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setHeaderColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setHeaders(ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setHeight(int) - Method in class bacnet.genomeBrowser.core.Region
setHeight(HashMap<String, Integer>) - Method in class bacnet.table.core.MatrixSize
setHeightDefault(int) - Method in class bacnet.table.core.MatrixSize
setHeightPix(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setHeightPix(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setHorizontalBarProperties() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite: Depending on Track parameters (Region and Zoom) fix properties of HorizontalBar
setId(String) - Method in class bacnet.datamodel.annotation.RfamElement
setId(String) - Method in class bacnet.datamodel.sequence.Sequence
setId(String) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
setID(String) - Method in class bacnet.datamodel.annotation.Signature
setInfo() - Method in class bacnet.table.gui.ColorMapperWizardPage
setInfoRead(boolean) - Method in class bacnet.datamodel.dataset.ExpressionData
setInfoRead(boolean) - Method in class bacnet.datamodel.dataset.NGS
setInitialized(boolean) - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
setInitView(String) - Method in class bacnet.Database
setInsoluble(boolean) - Method in class bacnet.datamodel.proteomics.NTerm
setIntersect(boolean) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setLabel_2(Label) - Method in class bacnet.sequenceTools.SrnaView
setLabel_3(Label) - Method in class bacnet.sequenceTools.SrnaView
setLblDescribedIn(Label) - Method in class bacnet.sequenceTools.SrnaView
setLblGene(Label) - Method in class bacnet.sequenceTools.SrnaView
setLblNodiff(Label) - Method in class bacnet.sequenceTools.GeneView
setLblNodiffProteome(Label) - Method in class bacnet.sequenceTools.GeneView
setLblOrAnyOther(Label) - Method in class bacnet.sequenceTools.SrnaView
setLblOveProteome(Label) - Method in class bacnet.sequenceTools.GeneView
setLblOver(Label) - Method in class bacnet.sequenceTools.GeneView
setLblOverProteomes(Label) - Method in class bacnet.sequenceTools.GeneView
setLblOverTranscriptomes(Label) - Method in class bacnet.sequenceTools.GeneView
setLblPredictedSecondaryStructure(Label) - Method in class bacnet.sequenceTools.SrnaView
setLblStructure(Label) - Method in class bacnet.sequenceTools.SrnaView
setLblTranscriptomesData(Label) - Method in class bacnet.sequenceTools.GeneView
setLblUnder(Label) - Method in class bacnet.sequenceTools.GeneView
setLblUnderProteome(Label) - Method in class bacnet.sequenceTools.GeneView
setLeftBCs(ArrayList<String>) - Method in class bacnet.scripts.core.Comparison
setLegend() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
setLength(int) - Method in class bacnet.datamodel.dataset.ExpressionData
setLength(int) - Method in class bacnet.datamodel.sequence.Sequence
setLengthAA(int) - Method in class bacnet.datamodel.sequence.Gene
setLineLength(int) - Method in class org.biojava3.core.sequence.io.FastaGeneWriter
setLineLength(int) - Method in class org.biojava3.core.sequence.io.FastaWriter
setLineSeparator(String) - Method in class org.biojava3.core.sequence.io.FastaWriter: Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
setLinkedBioCondition(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setListDatabases(HashMap<String, String>) - Method in class bacnet.Database
setListGenes(ArrayList<String>) - Method in class bacnet.sequenceTools.GeneView
setListSrnas(ArrayList<String>) - Method in class bacnet.sequenceTools.SrnaView
setLoaded(boolean) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setLocalization(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setLocation(SequenceLocation<S, C>) - Method in class org.biojava3.core.sequence.features.AbstractFeature: A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
setLocation(SequenceLocation<S, C>) - Method in interface org.biojava3.core.sequence.features.FeatureInterface: The new location for this feature.
setLocusTagToGeneNameMap(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.Chromosome
setLocusTagToGeneNameMap(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setLocusTagToOldLocusTagMap(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.Chromosome
setLogfcOmicsMatrix(ExpressionMatrix) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setLogFCProteomeTable(HashMap<String, ExpressionMatrix>) - Method in class bacnet.Database
setLogFCTable(HashMap<String, ExpressionMatrix>) - Method in class bacnet.Database
setLogo(String) - Method in class bacnet.Database
setLogTransformed(boolean) - Method in class bacnet.datamodel.dataset.NGS
setLongName(String) - Method in class org.biojava3.core.sequence.compound.CodonCompound
setLongName(String) - Method in class org.biojava3.core.sequence.template.AbstractCompound
setLongName(String) - Method in interface org.biojava3.core.sequence.template.Compound
setLongName(String) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
setLongName(String) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
setLowercaseToNull(ProteinSequence, Object[]) - Static method in class org.biojava3.core.sequence.io.CasePreservingProteinSequenceCreator: Takes a ProteinSequence which was created by a CasePreservingProteinSequenceCreator.
setMappingFrame(NTerm.MappingFrame) - Method in class bacnet.datamodel.proteomics.NTerm
setMarkup(Composite) - Static method in class bacnet.utils.RWTUtils
setMarkup(Label) - Static method in class bacnet.utils.RWTUtils
setMassSpecData(NTermData) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setMatrices(ArrayList<ExpressionMatrix>) - Method in class bacnet.datamodel.expdesign.BioCondition
setMatrix(ExpressionMatrix) - Method in class bacnet.datamodel.dataset.ExpressionData
setMatrix(ExpressionMatrix) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setMatrix(ExpressionMatrix) - Method in class bacnet.table.core.Filter
setMatrix(ExpressionMatrix) - Method in class bacnet.table.core.FilterList
setMatrix(ExpressionMatrix) - Method in class bacnet.utils.Filter
setMatrixDisplayed(ExpressionMatrix) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setMax(double) - Method in class bacnet.datamodel.dataset.ExpressionData
setMax(double) - Method in class bacnet.table.core.ColorMapper
setMax(double) - Method in class bacnet.table.core.ColorMapperRCP
setMaxColor(Color) - Method in class bacnet.table.core.ColorMapper
setMaxColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setMaxColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setMaxColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setMaxPos(double) - Method in class bacnet.table.core.ColorMapper
setMaxPos(double) - Method in class bacnet.table.core.ColorMapperRCP
setMaxQuant(String) - Method in class bacnet.datamodel.proteomics.NTerm
setMaxQuantum(String[]) - Method in class bacnet.datamodel.proteomics.NTerm
setMean(double) - Method in class bacnet.datamodel.dataset.ExpressionData
setMean(double) - Method in class bacnet.table.core.ColorMapper
setMean(double) - Method in class bacnet.table.core.ColorMapperRCP
setMedia(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setMediaGrowthProperties(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setMedian(double) - Method in class bacnet.datamodel.dataset.ExpressionData
setMedian(double) - Method in class bacnet.table.core.ColorMapper
setMedian(double) - Method in class bacnet.table.core.ColorMapperRCP
setMedianValue(String, double) - Method in class bacnet.datamodel.dataset.GeneExpression: Set the median value of corresponding probe in double[][] values
setMiddleH(int) - Method in class bacnet.genomeBrowser.core.Region
setMiddleV(int) - Method in class bacnet.genomeBrowser.core.Region
setMidLeftColor(Color) - Method in class bacnet.table.core.ColorMapper
setMidLeftColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setMidLeftColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setMidLeftColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setMidLeftPos(double) - Method in class bacnet.table.core.ColorMapper
setMidLeftPos(double) - Method in class bacnet.table.core.ColorMapperRCP
setMidRightColor(Color) - Method in class bacnet.table.core.ColorMapper
setMidRightColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setMidRightColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setMidRightColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setMidRightPos(double) - Method in class bacnet.table.core.ColorMapper
setMidRightPos(double) - Method in class bacnet.table.core.ColorMapperRCP
setMin(double) - Method in class bacnet.datamodel.dataset.ExpressionData
setMin(double) - Method in class bacnet.table.core.ColorMapper
setMin(double) - Method in class bacnet.table.core.ColorMapperRCP
setMinColor(Color) - Method in class bacnet.table.core.ColorMapper
setMinColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setMinColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setMinColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setMinimumAlpha(GC) - Static method in class bacnet.genomeBrowser.tracksGUI.GElement: Set Alpha to 15
setMinPos(double) - Method in class bacnet.table.core.ColorMapper
setMinPos(double) - Method in class bacnet.table.core.ColorMapperRCP
setModifications(HashMap<String, ArrayList<NTerm>>) - Method in class bacnet.datamodel.dataset.NTermData
setModifs(ArrayList<NTerm.TypeModif>) - Method in class bacnet.datamodel.proteomics.TIS
setModifSequence(String) - Method in class bacnet.datamodel.proteomics.NTerm
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.compound.CodonCompound
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.template.AbstractCompound
setMolecularWeight(Float) - Method in interface org.biojava3.core.sequence.template.Compound
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
setMolecularWeight(Float) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
setMolMass(double) - Method in class bacnet.datamodel.sequence.Gene
setMouseXPosition(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setMouseXPosition(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setMouseYPosition(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setMouseYPosition(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setMultiFasta(ArrayList<String>) - Method in class bacnet.datamodel.sequence.Genome.GetMultiFastaThread
setMutant(ArrayList<String>) - Method in class bacnet.datamodel.expdesign.BioCondition
setName(String) - Method in class bacnet.datamodel.annotation.RfamElement
setName(String) - Method in class bacnet.datamodel.annotation.Signature
setName(String) - Method in class bacnet.datamodel.dataset.OmicsData
setName(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setName(String) - Method in class bacnet.datamodel.expdesign.Experiment
setName(String) - Method in class bacnet.datamodel.sequence.Chromosome
setName(String) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setName(String) - Method in class bacnet.datamodel.sequence.Sequence
setName(String) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setName(String) - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
setName(String) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setName(String) - Method in class bacnet.table.core.Filter
setName(String) - Method in class bacnet.utils.Filter
setNameMassSpecDataFinal(String) - Method in class bacnet.scripts.listeriomics.nterm.NTermCreateFinalData
setNameNTermData(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setNameRawData(String) - Method in class bacnet.datamodel.proteomics.NTermCreateData
setNavigationListener(BrowserNavigationListener) - Method in class bacnet.Database
setNbElements(int) - Method in class bacnet.table.core.ColorMapper
setNbElements(int) - Method in class bacnet.table.core.ColorMapperRCP
setNbElementType(int) - Method in class bacnet.datamodel.annotation.Annotation
setNbSet(int) - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
setNcRNAs(LinkedHashMap<String, NcRNA>) - Method in class bacnet.datamodel.sequence.Chromosome
setNewChromosome(String) - Method in class bacnet.genomeBrowser.core.Track
setNewLocusTag(String) - Method in class bacnet.datamodel.sequence.Gene
setNextCodon(String) - Method in class bacnet.datamodel.proteomics.NTerm
setNGSSeqs(ArrayList<NGS>) - Method in class bacnet.datamodel.expdesign.BioCondition
setNoData(boolean) - Method in class bacnet.datamodel.expdesign.BioCondition
setNoDNAList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setNoncodingSequenceHashMap(LinkedHashMap<String, DNASequence>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setNoProtList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setNoRNAList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setNotDiffExpressedASrnas(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setNotDiffExpressedCisRegs(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setNotDiffExpressedGenes(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setNotDiffExpresseds(TreeSet<String>) - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
setNotDiffExpressedSrnas(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setNote(String) - Method in class bacnet.datamodel.annotation.RfamElement
setNote(String) - Method in class bacnet.datamodel.dataset.OmicsData
setNotesList(ArrayList<String>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setnTermExp(NTermData) - Method in class bacnet.datamodel.proteomics.NTermFilter
setnTermHighlight(NTerm) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setNTermInfo(NTerm, NTermData) - Method in class bacnet.genomeBrowser.CompositeNTermInfo: Set all Labels for NTerm info
setnTermRef(NTerm) - Method in class bacnet.datamodel.proteomics.TIS
setnTerms(ArrayList<NTermData>) - Method in class bacnet.datamodel.expdesign.BioCondition
setnTerms(ArrayList<NTerm>) - Method in class bacnet.datamodel.proteomics.TIS
setnTermTypeOverlap(String) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setNucleotide(boolean) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setOldLocusTag(String) - Method in class bacnet.datamodel.sequence.Gene
setOperon(String) - Method in class bacnet.datamodel.sequence.Gene
setOperons(ArrayList<Operon>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setOperons(LinkedHashMap<String, Operon>) - Method in class bacnet.datamodel.sequence.Chromosome
setOrdered(boolean) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setOrdered(boolean, ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setOrderedRowNames(ArrayList<String>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setOriginalHeader(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setOverASrnas(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setOverBioConds(TreeSet<String>) - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
setOverCisRegs(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setOverGenes(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setOverlap(String) - Method in class bacnet.datamodel.proteomics.NTerm
setOverlapInFrame(boolean) - Method in class bacnet.datamodel.proteomics.NTerm
setOverlapingGene(String) - Method in class bacnet.datamodel.proteomics.TIS
setOverlaps(ArrayList<String>) - Method in class bacnet.datamodel.proteomics.TIS
setOverSrnas(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setParentDNASequence(AbstractSequence, Integer, Integer) - Method in class org.biojava3.core.sequence.ProteinSequence: A Protein sequence can be stand alone or loaded from a transcript sequence.
setParentFeature(FeatureInterface<S, C>) - Method in class org.biojava3.core.sequence.features.AbstractFeature: A feature can be the child or contained by a parent feature.
setParentFeature(FeatureInterface<S, C>) - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Set the parent feature
setParentGenome(Genome) - Method in class bacnet.datamodel.sequence.Chromosome
setParentGenome(GenomeNCBI) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setParentSequence(AbstractSequence<C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setParentViewId(String) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
setPartService(EPartService) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setPath(String) - Method in class bacnet.Database
setPATH(String) - Static method in class bacnet.datamodel.dataset.ExpressionData
setPeptides(HashMap<String, ArrayList<NTerm>>) - Method in class bacnet.datamodel.dataset.NTermData: Link peptideSequence to ArrayList(NTerm)
This correspond to the list of NTerm having same peptideSequence
setPreloadedItems(Composite) - Static method in class bacnet.utils.RWTUtils
setPreviousCodon(String) - Method in class bacnet.datamodel.proteomics.NTerm
setPrideLink(String) - Static method in class bacnet.utils.RWTUtils
setProbes(TreeMap<Integer, Integer>) - Method in class bacnet.datamodel.dataset.Tiling
setProbes(TreeMap<String, Integer>) - Method in class bacnet.datamodel.dataset.GeneExpression
setProbesGExpression(TreeMap<String, Integer>) - Method in class bacnet.Database
setProbesTiling(TreeMap<Integer, Integer>) - Method in class bacnet.Database
setProduct(String) - Method in class bacnet.datamodel.sequence.Gene
setProduct(String) - Method in class bacnet.datamodel.sequence.NcRNA
setProjectName(String) - Method in class bacnet.Database
setProperties(LinkedHashMap<String, String>) - Method in class org.biojava3.core.sequence.features.DBReferenceInfo
setProtein_id(String) - Method in class bacnet.datamodel.sequence.Gene
setProteinIDTolocusTag(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.Chromosome
setProteinIDToOldLocusTagMap(LinkedHashMap<String, String>) - Method in class bacnet.datamodel.sequence.Chromosome
setProteinNCBILink(String) - Static method in class bacnet.utils.RWTUtils
setProteomes(ArrayList<ProteomicsData>) - Method in class bacnet.datamodel.expdesign.BioCondition
setProteomes(HashMap<String, Boolean>) - Method in class bacnet.scripts.database.DataValidation
setProteomesArrayPath(String) - Method in class bacnet.Database
setProteomesComparisonsArrayPath(String) - Method in class bacnet.Database
setProxySequenceReader(SequenceReader<C>) - Method in class org.biojava3.core.sequence.template.AbstractSequence: Very important method that allows external mappings of sequence data and features.
setPseudogene(boolean) - Method in class bacnet.datamodel.sequence.Gene
setPubMedLink(String) - Static method in class bacnet.utils.RWTUtils
setQualities(List<Number>) - Method in class org.biojava3.core.sequence.features.QualityFeature
setQuantities(List<Number>) - Method in class org.biojava3.core.sequence.features.QuantityFeature
setRawDatas(ArrayList<String>) - Method in class bacnet.datamodel.dataset.OmicsData
setRead(boolean[]) - Method in class bacnet.datamodel.dataset.ExpressionData
setRed(int) - Method in class bacnet.table.core.ColorSWT
setRef(String) - Method in class bacnet.datamodel.sequence.Sequence
setReference(String) - Method in class bacnet.datamodel.annotation.Signature
setReference(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setRefSequence(String) - Method in class bacnet.datamodel.proteomics.TIS
setRelativeValueDisplay() - Method in class bacnet.genomeBrowser.TestGenomeBrowser
setRightBCs(ArrayList<String>) - Method in class bacnet.scripts.core.Comparison
setRowNameCellColor(Color) - Method in class bacnet.table.core.ColorMapper
setRowNames(TreeMap<String, Integer>) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setRowNameTextColor(Color) - Method in class bacnet.table.core.ColorMapper
setScore(double) - Method in class bacnet.datamodel.annotation.RfamElement
setScore(int) - Method in class bacnet.datamodel.proteomics.NTerm
setScrolledComposite(ScrolledComposite) - Method in class bacnet.genomeBrowser.dialog.LegendDialog
setScrolledComposite(ScrolledComposite) - Method in class bacnet.sequenceTools.SrnaView
setSDBindingEnergy() - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: For every gene calculate the SD-aSD hybridization affinity and save it in: /StatGenes/aSDBindingEneryg.excel
setSearchText(String) - Method in class bacnet.table.gui.TableFilter
setSecondRowName(String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setSelectedGenes(ArrayList<String>) - Method in class bacnet.sequenceTools.AnnotationView
setSeq(Srna) - Method in class bacnet.sequenceTools.SrnaView
setSequence(Gene) - Method in class bacnet.sequenceTools.GeneView
setSequence(String) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setSequence(String) - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
setSequence(String) - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
setSequenceCollection(SequenceOptimizationHints.SequenceCollection) - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
setSequenceMap(String) - Method in class bacnet.datamodel.proteomics.NTerm
setSequencePeptide(String) - Method in class bacnet.datamodel.proteomics.NTerm
setSequenceScore(Double) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setSequenceUsage(SequenceOptimizationHints.SequenceUsage) - Static method in class org.biojava3.core.sequence.SequenceOptimizationHints
setSetNames(ArrayList<String>) - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
setSets(TreeMap<String, ArrayList<String>>) - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
setShell(Shell) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setShortDescription(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature
setShortDescription(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Set the short description that can be used to describe the feature
setShortName(String) - Method in class org.biojava3.core.sequence.compound.CodonCompound
setShortName(String) - Method in class org.biojava3.core.sequence.template.AbstractCompound
setShortName(String) - Method in interface org.biojava3.core.sequence.template.Compound
setShortName(String) - Method in class org.biojava3.core.sequence.transcription.CaseInsensitiveCompound
setShortName(String) - Method in class org.biojava3.core.sequence.transcription.Table.Codon
setSignature(Signature) - Method in class bacnet.expressionAtlas.core.SignatureSelectionDialog
setSignatures(TreeSet<String>) - Method in class bacnet.datamodel.sequence.Sequence
setSignaturesNametoID(TreeMap<String, String>) - Method in class bacnet.Database
setSize(int) - Method in class bacnet.datamodel.annotation.Signature
setSoluble(boolean) - Method in class bacnet.datamodel.proteomics.NTerm
setSource(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature: Set the feature source
setSource(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Change the source of the FeatureInterface.
setSource(String) - Method in class org.biojava3.core.sequence.template.AbstractSequence: Added support for the source of this sequence for GFF3 export
setSpecies(String) - Method in class bacnet.Database
setSpecies(String) - Method in class bacnet.datamodel.annotation.RfamElement
setSpecies(String) - Method in class bacnet.datamodel.sequence.Genome
setSpecies(String) - Method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
setSpectra(int) - Method in class bacnet.datamodel.proteomics.NTerm
setSpectrum(int[]) - Method in class bacnet.datamodel.proteomics.NTerm
setSrnaLink(String, HashMap<String, String>) - Static method in class bacnet.utils.RWTUtils
setsRNAListEGDe(ArrayList<String>) - Method in class bacnet.Database
setSrnaOrder() - Static method in class bacnet.datamodel.sequence.Srna: Classify Srna par IDs and save it in PATH_LISTSRNA
setsRNAs(ArrayList<Srna>) - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
setsRNAs(LinkedHashMap<String, Srna>) - Method in class bacnet.datamodel.sequence.Chromosome
setStartCode(String) - Method in class bacnet.datamodel.proteomics.NTerm
setStartCodon(String) - Method in class bacnet.datamodel.proteomics.NTerm
setStat() - Method in class bacnet.datamodel.dataset.ExpressionData: Set statistical parameters using values array
setStat() - Method in class bacnet.table.core.ColorMapper
setStat() - Method in class bacnet.table.core.ColorMapperRCP
setStatDataColor() - Method in class bacnet.table.core.ColorMapper
setStatDataColor() - Method in class bacnet.table.core.ColorMapperRCP
setStatDataValues() - Method in class bacnet.table.core.ColorMapper
setStatDataValues() - Method in class bacnet.table.core.ColorMapperRCP
setStatMapper() - Method in class bacnet.table.core.ColorMapper: Set parameters corresponding to stat data i.e. value from 0 to 1
setStatMapper() - Method in class bacnet.table.core.ColorMapperRCP: Set parameters corresponding to stat data i.e. value from 0 to 1
setStatTable(ExpressionMatrix) - Method in class bacnet.Database
setStdevDataColor() - Method in class bacnet.table.core.ColorMapper
setStdevDataColor() - Method in class bacnet.table.core.ColorMapperRCP
setStrand(char) - Method in class bacnet.datamodel.annotation.RfamElement
setStrand(char) - Method in class bacnet.datamodel.sequence.Sequence
setStrand(Strand) - Method in class bacnet.sequenceTools.SequenceDisplayDialog
setStrand(Strand) - Method in class org.biojava3.core.sequence.GeneSequence
setStudyName(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setSubsetNames(ArrayList<String>) - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
setSubsets(TreeMap<String, ArrayList<String>>) - Method in class bacnet.scripts.core.vennDiagram.VennDiagram
setSynonym(TreeSet<String>) - Method in class bacnet.datamodel.sequence.Sequence
setTabFolder(TabFolder) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setTabFolder(TabFolder) - Method in class bacnet.sequenceTools.GeneView
setTabFolder(TabFolder) - Method in class bacnet.sequenceTools.SrnaView
setTabFolder(TabFolder) - Method in class bacnet.views.CoExprNetworkView
setTable(Table) - Method in class bacnet.genomeBrowser.dialog.LegendDialog
setTableBioCondition(TableViewer) - Method in class bacnet.genomeBrowser.NTerminomicsView
setTableBioCondition(TableViewer) - Method in class bacnet.sequenceTools.AnnotationView
setTableBioCondition(Table) - Method in class bacnet.genomeBrowser.dialog.LegendDialog
setTableComposite(TableCompositeHeatMap) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setTableComposite(TableCompositeHeatMap) - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
setTableComposite(TableCompositeHeatMap) - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
setTableComposite(TableCompositeHeatMap) - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
setTableComposite(TableSWTComposite) - Method in class bacnet.table.TableSWTView
setTableElementName(String) - Method in class bacnet.table.core.Filter
setTableElementName(String) - Method in class bacnet.utils.Filter
setTableGenes(Table) - Method in class bacnet.sequenceTools.GeneView
setTableGenes(Table) - Method in class bacnet.views.CoExprNetworkView
setTableNodiff(Table) - Method in class bacnet.sequenceTools.GeneView
setTableNodiffProteome(Table) - Method in class bacnet.sequenceTools.GeneView
setTableOtherInfo(Table) - Method in class bacnet.sequenceTools.SrnaView
setTableOver(Table) - Method in class bacnet.sequenceTools.GeneView
setTableOverProteome(Table) - Method in class bacnet.sequenceTools.GeneView
setTableProteomes(Table) - Method in class bacnet.sequenceTools.GeneView
setTableSrnas(Table) - Method in class bacnet.sequenceTools.SrnaView
setTableTranscriptomes(Table) - Method in class bacnet.sequenceTools.GeneView
setTableUnder(Table) - Method in class bacnet.sequenceTools.GeneView
setTableUnderProteome(Table) - Method in class bacnet.sequenceTools.GeneView
setTaxonomy(TaxonomyID) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setTbtmGraphVisualization(TabItem) - Method in class bacnet.views.CoExprNetworkView
setTbtmHeatmap(TabItem) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setTbtmScatterPlot(TabItem) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setTemperature(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setTestData(boolean) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setTests(ArrayList<StatTest>) - Method in class bacnet.scripts.core.Comparison
setText(String) - Method in class bacnet.raprcp.DownloadServiceHandler
setTextColor(Color) - Method in class bacnet.table.core.ColorMapper
setTextColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setTextColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setTextColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setTextCutOff(Text) - Method in class bacnet.views.CoExprNetworkView
setTextHeaderColor(Color) - Method in class bacnet.table.core.ColorMapperRCP
setTextHeaderColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapper
setTextHeaderColorSWT(ColorSWT) - Method in class bacnet.table.core.ColorMapperRCP
setTextSearch(Text) - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
setTextSearch(Text) - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
setThreadPool(ThreadPoolExecutor) - Static method in class org.biojava3.core.util.ConcurrencyTools: Sets thread pool to any given ThreadPoolExecutor to allow use of an alternative execution style.
setThreadPoolCPUsAvailable(int) - Static method in class org.biojava3.core.util.ConcurrencyTools: Sets thread pool to reserve a given number of processor cores for foreground or other use.
setThreadPoolCPUsFraction(float) - Static method in class org.biojava3.core.util.ConcurrencyTools: Sets thread pool to a given fraction of the available processors.
setThreadPoolDefault() - Static method in class org.biojava3.core.util.ConcurrencyTools: Sets thread pool to default of 1 background thread for each processor core.
setThreadPoolSingle() - Static method in class org.biojava3.core.util.ConcurrencyTools: Sets thread pool to a single background thread.
setThreadPoolSize(int) - Static method in class org.biojava3.core.util.ConcurrencyTools: Sets thread pool to given size.
setThreshold(int) - Method in class bacnet.datamodel.proteomics.NTerm
setTiling(boolean) - Method in class bacnet.scripts.core.Comparison
setTilings(ArrayList<Tiling>) - Method in class bacnet.datamodel.expdesign.BioCondition
setTime(String) - Method in class bacnet.datamodel.expdesign.BioCondition
setTIRSequence() - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: We create a fasta file with all the TIR DNA sequence (-18 +63)
setTIRStructureEnergy() - Method in class bacnet.scripts.listeriomics.nterm.NTermStat: For every gene calculate the 2nd structure free energy and save it a table
We calculate the energy for 40 different sequence: -20+40 to -20+80 and calculate the average energy
setTisList(ArrayList<TIS>) - Method in class bacnet.datamodel.dataset.NTermData
setTisMap(HashMap<NTerm, TIS>) - Method in class bacnet.datamodel.dataset.NTermData
setTISName(String) - Method in class bacnet.datamodel.proteomics.NTerm
setTitle(String) - Method in class bacnet.views.InternalBrowser
setToolBar(ToolBar) - Method in class bacnet.e4.rap.BannerView
setTotalBP(int) - Method in class bacnet.genomeBrowser.core.Zoom
setTotalSpectra(int) - Method in class bacnet.datamodel.proteomics.TIS
setTrack(Track) - Method in class bacnet.genomeBrowser.core.DataTrack
setTrack(Track) - Method in class bacnet.genomeBrowser.dialog.AddProteomicsDataDialog
setTrack(Track) - Method in class bacnet.genomeBrowser.dialog.AddTranscriptomicsDataDialog
setTrack(Track) - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
setTrack(Track) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData: Set the data of the Canvas, and implement the PaintListener Execute different tasks:
Fix the number of pixel for one base pair Set width and height parameters for data and annotation track Display in order:
different line and ticks for the base pair position, every display needed in the background display all the data display sequence if needed display annotation different genome name and mouse line in foreground
setTrack(Track) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome: Set the data of the Canvas, and implement the PaintListener Execute different tasks:
Fix the number of pixel for one base pair Set width and height parameters for data and annotation track Display in order:
different line and ticks for the base pair position, every display needed in the background display all the data display sequence if needed display annotation different genome name and mouse line in foreground
setTrack(Track) - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
setTrackComposite(Composite) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setTrackGenome(Track) - Method in class bacnet.sequenceTools.GeneView
setTracksComposite(TracksComposite) - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
setTranscriptomes(HashMap<String, Boolean>) - Method in class bacnet.scripts.database.DataValidation
setTranscriptomesArrayPath(String) - Method in class bacnet.Database
setTranscriptomesComparisonsArrayPath(String) - Method in class bacnet.Database
setTranscriptomics(boolean) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
setTssDownCoverage(int) - Method in class bacnet.datamodel.proteomics.NTerm
setTssDownDistance(int) - Method in class bacnet.datamodel.proteomics.NTerm
setTssDowntype(String) - Method in class bacnet.datamodel.proteomics.NTerm
setTssUpCoverage(int) - Method in class bacnet.datamodel.proteomics.NTerm
setTssUpDistance(int) - Method in class bacnet.datamodel.proteomics.NTerm
setTssUptype(String) - Method in class bacnet.datamodel.proteomics.NTerm
setTxtCutoffLogFC(Text) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setTxtCutoffLogFC(Text) - Method in class bacnet.sequenceTools.GeneView
setTxtCutoffLogFCProteome(Text) - Method in class bacnet.sequenceTools.GeneView
setTxtCutoffPvalue(Text) - Method in class bacnet.sequenceTools.GeneView
setTxtSearch(Text) - Method in class bacnet.genomeBrowser.NTerminomicsView
setTxtSearch(Text) - Method in class bacnet.sequenceTools.AnnotationView
setTxtSearch(Text) - Method in class bacnet.sequenceTools.GenomicsView
setTxtSeqnucleotide(Text) - Method in class bacnet.sequenceTools.SrnaView
setType(OmicsData.TypeData) - Method in class bacnet.datamodel.dataset.OmicsData
setType(Sequence.SeqType) - Method in class bacnet.datamodel.sequence.Sequence
setType(StatTest.TypeStat) - Method in class bacnet.scripts.core.stat.StatTest
setType(ColorMapper.TypeMapper) - Method in class bacnet.table.core.ColorMapper
setType(ColorMapperRCP.Type) - Method in class bacnet.table.core.ColorMapperRCP
setType(String) - Method in class bacnet.datamodel.annotation.RfamElement
setType(String) - Method in class bacnet.datamodel.annotation.Signature
setType(String) - Method in class org.biojava3.core.sequence.features.AbstractFeature: Set the feature type
setType(String) - Method in interface org.biojava3.core.sequence.features.FeatureInterface: Change the type of this feature.
setTypeData(OmicsData.TypeData) - Method in class bacnet.scripts.core.Expression
setTypeDataContained(TreeSet<OmicsData.TypeData>) - Method in class bacnet.datamodel.expdesign.BioCondition
setTypeFilter(Filter.TypeFilter) - Method in class bacnet.table.core.Filter
setTypeFilter(Filter.TypeFilter) - Method in class bacnet.utils.Filter
setTypeModif(NTerm.TypeModif) - Method in class bacnet.datamodel.proteomics.NTerm
setTypeNcRNA(NcRNA.TypeNcRNA) - Method in class bacnet.datamodel.sequence.NcRNA
setTypeOverlap(String) - Method in class bacnet.datamodel.proteomics.NTerm
setTypeOverlaps(ArrayList<String>) - Method in class bacnet.datamodel.dataset.NTermData
setTypeOverlaps(ArrayList<String>) - Method in class bacnet.datamodel.proteomics.NTermFilter
setTypeSrna(Srna.TypeSrna) - Method in class bacnet.datamodel.sequence.Srna
setUnderASrnas(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setUnderBioConds(TreeSet<String>) - Method in class bacnet.expressionAtlas.core.GenomeElementAtlas
setUnderCisRegs(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setUnderGenes(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setUnderSrnas(String[]) - Method in class bacnet.expressionAtlas.core.ComparisonAtlas
setUniprotbaseURL(String) - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
setUniprotDirectoryCache(String) - Static method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
setUpDNAList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
SetupPart - Class in bacnet.e4.rap.setup: SetupPart for initialisation and creation of the Database
SetupPart() - Constructor for class bacnet.e4.rap.setup.SetupPart
setUpProtList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setUpRNAList(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setUserCollection(Collection<Object>) - Method in class org.biojava3.core.sequence.template.AbstractSequence
setUserObject(Object) - Method in class org.biojava3.core.sequence.features.AbstractFeature: Allow the user to associate an object with the feature.
setUserObject(Object) - Method in interface org.biojava3.core.sequence.features.FeatureInterface
setValue(double, int, int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setValue(double, String, String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setValue(int, double) - Method in class bacnet.datamodel.dataset.Tiling
setValueAnnotation(String, String, String) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setValues(double[]) - Method in class bacnet.datamodel.dataset.ExpressionData
setValues(double[]) - Method in class bacnet.table.core.ColorMapper
setValues(double[]) - Method in class bacnet.table.core.ColorMapperRCP
setValues(double[][]) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
setValues(int, int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: Create new double[][] values with nbRow and nbColumn All value will then be equal to 0
setValues(ExpressionMatrix) - Method in class bacnet.table.core.ColorMapper
setValues(ExpressionMatrix) - Method in class bacnet.table.core.ColorMapperRCP
setVar(double) - Method in class bacnet.table.core.ColorMapper
setVar(double) - Method in class bacnet.table.core.ColorMapperRCP
setVariables() - Method in class bacnet.Database: MOST IMPORTANT INIT METHOD : Set all variables for the website
setVariance(double) - Method in class bacnet.datamodel.dataset.ExpressionData
setVerticalBarProperties() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite: Depending on CanvasData parameters fix properties of VerticalBar
setVertices(HashMap<String, String>) - Method in class bacnet.datamodel.dataset.Network: List of vertices = genome elements + their attributes = genome position, type, annotation
setViewId(String) - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
setViewId(String) - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
setViewId(String) - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
setViewId(String) - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
setViewId(String) - Method in class bacnet.sequenceTools.SrnaView
setViewID(String) - Method in class bacnet.sequenceTools.AnnotationView
setViewID(String) - Method in class bacnet.sequenceTools.GeneView
setWebpageTitle(String) - Method in class bacnet.Database
setWidth(int) - Method in class bacnet.genomeBrowser.core.Region
setWidth(HashMap<String, Integer>) - Method in class bacnet.table.core.MatrixSize
setWidthBP(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
setWidthBP(int) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
setWidthDefault(int) - Method in class bacnet.table.core.MatrixSize
setWidthRowNameDefault(int) - Method in class bacnet.table.core.MatrixSize
setWildType(boolean) - Method in class bacnet.datamodel.expdesign.BioCondition
setX1(int) - Method in class bacnet.genomeBrowser.core.Region
setX2(int) - Method in class bacnet.genomeBrowser.core.Region
setY1(int) - Method in class bacnet.genomeBrowser.core.Region
setY2(int) - Method in class bacnet.genomeBrowser.core.Region
setZoom(Zoom) - Method in class bacnet.genomeBrowser.core.Track
setZoomChangedFlag(boolean) - Method in class bacnet.genomeBrowser.core.Zoom
setZoomHeightMax(int) - Method in class bacnet.genomeBrowser.core.Zoom
setZoomHeightPosition(int) - Method in class bacnet.genomeBrowser.core.Zoom
setZoomNumber(int) - Method in class bacnet.genomeBrowser.core.Zoom
setZoomPosition(int) - Method in class bacnet.genomeBrowser.core.Zoom
setZoomPosition(Region) - Method in class bacnet.genomeBrowser.core.Zoom: Search the zoom position which correspond the best to displayRegion DisplayRegion should be inferior to display range given by the zoom
setZoomRatio(double) - Method in class bacnet.genomeBrowser.core.Zoom
setZoomVertical(double) - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
showAllLocusID() - Static method in class bacnet.scripts.database.GenomesCreation
showHelp(String, EPartService) - Static method in class bacnet.views.HelpPage: Show the help page in an external browser
showInfoPanel() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite: Show the info Panel showing NTerm data
showSearchPath() - Static method in class bacnet.scripts.blast.Blast
shuffle(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.
shutdown() - Static method in class org.biojava3.core.util.ConcurrencyTools: Disables new tasks from being submitted and closes the thread pool cleanly.
shutdownAndAwaitTermination() - Static method in class org.biojava3.core.util.ConcurrencyTools: Closes the thread pool.
Signature - Class in bacnet.datamodel.annotation
Signature() - Constructor for class bacnet.datamodel.annotation.Signature
SignatureSelectionDialog - Class in bacnet.expressionAtlas.core
SignatureSelectionDialog(Shell) - Constructor for class bacnet.expressionAtlas.core.SignatureSelectionDialog: Create the dialog.
SimpleLocation - Class in org.biojava3.core.sequence.location: Very basic implementation of the Location interface which defines a series of simple constructors.
SimpleLocation(int, int) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(int, int, Strand) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(int, int, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand, boolean, boolean) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand, boolean, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand, boolean, AccessionID) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand, AccessionID) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimpleLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.SimpleLocation
SimplePoint - Class in org.biojava3.core.sequence.location: Basic implementation of the Point interface.
SimplePoint(int) - Constructor for class org.biojava3.core.sequence.location.SimplePoint
SimplePoint(int, boolean, boolean) - Constructor for class org.biojava3.core.sequence.location.SimplePoint
SingleCompoundSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage: An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet).
SingleCompoundSequenceReader(C, CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Build the object with a compound rather than a String
SingleCompoundSequenceReader(String, CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader: Public constructor to be used with String based constructor
SINGULARITY_PATH - Variable in class bacnet.views.CRISPRPredictView
SINGULARITY_PATH - Variable in class bacnet.views.CRISPRPredictView2
sir_graph - Static variable in class bacnet.scripts.core.UNAfold
sir_graph - Static variable in class bacnet.utils.UNAfold
size() - Method in class org.biojava3.core.util.FlatFileCache
size() - Method in class org.biojava3.core.util.SoftHashMap
skip(long) - Method in class org.biojava3.core.sequence.io.BufferedReaderBytesRead: Skips characters.
skip(long) - Method in class org.biojava3.core.util.UncompressInputStream
SmallPeptidesSearch - Class in bacnet.scripts.listeriomics.srna: Deprecated.
SmallPeptidesSearch() - Constructor for class bacnet.scripts.listeriomics.srna.SmallPeptidesSearch: Deprecated.
SMIRNOV - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
SoftHashMap<K,V> - Class in org.biojava3.core.util: A in memory cache using soft references.
SoftHashMap() - Constructor for class org.biojava3.core.util.SoftHashMap
SoftHashMap(int) - Constructor for class org.biojava3.core.util.SoftHashMap
sort(int) - Method in class bacnet.datamodel.dataset.ExpressionMatrix
sort(int, boolean) - Method in class bacnet.datamodel.dataset.ExpressionMatrix: TO IMPROVE
Sort double[][] values Using sorted array, reorder rows through OrderedRowNames
sortByStart() - Method in class org.biojava3.genome.parsers.gff.FeatureList: Create a new list that is ordered by the starting index of the features' locations.
sortColumn(double[][], int) - Static method in class bacnet.utils.ArrayUtils: Sort an array using column given by the index
sortColumn(String[][], int, boolean) - Static method in class bacnet.utils.ArrayUtils: Sort a column inside a String[][] array

WARNING: if two values are the same in the column, it will display only the first one with this value in the sorted array
source() - Method in class org.biojava3.genome.parsers.gff.Feature: Get source (aka method).
SPEARCORR - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
splice(DNASequence) - Method in class org.biojava3.genome.parsers.gff.FeatureList: Concatenate successive portions of the specified sequence using the feature locations in the list.
SplitFasta - Class in org.biojava3.genome.util: Utility to write each Fasta entry to a unique file
SplitFasta() - Constructor for class org.biojava3.genome.util.SplitFasta
square(double[][]) - Static method in class bacnet.utils.ArrayUtils: Return array Y=(x_ij ^ 2)
squareVector(double[]) - Static method in class bacnet.utils.VectorUtils: Calcul of the square of a vector
Srna - Class in bacnet.datamodel.sequence
Srna - Enum constant in enum bacnet.datamodel.sequence.Sequence.SeqType
Srna - Enum constant in enum bacnet.datamodel.sequence.Srna.TypeSrna
Srna() - Constructor for class bacnet.datamodel.sequence.Srna
Srna(String, int, int) - Constructor for class bacnet.datamodel.sequence.Srna
Srna(String, int, int, char) - Constructor for class bacnet.datamodel.sequence.Srna
SRNA_NUMBER - Static variable in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN
Srna.TypeSrna - Enum in bacnet.datamodel.sequence
Srna10403SOliver - Class in bacnet.scripts.listeriomics.srna
Srna10403SOliver() - Constructor for class bacnet.scripts.listeriomics.srna.Srna10403SOliver
SrnaAlignmentBlastN - Class in bacnet.scripts.listeriomics.srna
SrnaAlignmentBlastN() - Constructor for class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN
sRNACircularGenome(int, int, Genome, String) - Method in class bacnet.scripts.genome.CircularGenomeJPanel
SrnaFinalList - Class in bacnet.scripts.listeriomics.srna
SrnaFinalList() - Constructor for class bacnet.scripts.listeriomics.srna.SrnaFinalList
SrnaListeriomics - Class in bacnet.scripts.listeriomics: List of methods to manage Srna data for Listeriomics
SrnaListeriomics() - Constructor for class bacnet.scripts.listeriomics.SrnaListeriomics
sRNAs - Variable in class bacnet.scripts.genome.CircularGenomeJPanel
SrnaSummaryView - Class in bacnet.sequenceTools
SrnaSummaryView() - Constructor for class bacnet.sequenceTools.SrnaSummaryView
SrnaTables - Class in bacnet.scripts.listeriomics.srna: Include a list of Methods to read every Table containing Small RNAs in Listeria
For each it reads the Table and create a List of Srna
SrnaTables() - Constructor for class bacnet.scripts.listeriomics.srna.SrnaTables
SrnaView - Class in bacnet.sequenceTools
SrnaView() - Constructor for class bacnet.sequenceTools.SrnaView
start() - Method in class org.biojava3.genome.parsers.gff.Location: Get starting index (origin 0).
start(BundleContext) - Method in class bacnet.e4.rap.setup.Activator
start(BundleContext) - Method in class bacnet.scripts.Activator
startCodon - Static variable in class bacnet.datamodel.sequence.Codon
startCodon(String) - Static method in class bacnet.datamodel.sequence.Codon: If it is a start codon return the corresponding codon, an empty String otherwise
StartCodonProfile - Class in bacnet.scripts.genome: Calculate presence of start codon on firrst chromosome of bacterial genomes
StartCodonProfile() - Constructor for class bacnet.scripts.genome.StartCodonProfile
StartCodonSequence - Class in org.biojava3.core.sequence: Used to map the start codon feature on a gene
StartCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava3.core.sequence.StartCodonSequence
startsAfter(Location) - Method in class org.biojava3.genome.parsers.gff.Location: Check if this location starts after the other location starts.
startsBefore(Location) - Method in class org.biojava3.genome.parsers.gff.Location: Check if this location starts before other location starts.
STAT - Enum constant in enum bacnet.table.core.ColorMapper.TypeMapper
STAT - Enum constant in enum bacnet.table.core.ColorMapperRCP.Type
statDatabase() - Static method in class bacnet.scripts.blast.ProteinTools: Extract statistics from existing databases, number of lmos, sRNA, utr...
statDatabase() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase: Extract statistics from existing databases, number of lmos, sRNA, utr...
statInternalORF(Genome) - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat: Given a genome extract main information such as:
number of start codons, stop codons number of high SD binding sites number of possible ORFs number of predicted genes

From this metrics, predict the number of possible internal translation initiation site
StatTest - Class in bacnet.scripts.core.stat
StatTest() - Constructor for class bacnet.scripts.core.stat.StatTest
StatTest(StatTest.TypeStat) - Constructor for class bacnet.scripts.core.stat.StatTest
StatTest.TypeStat - Enum in bacnet.scripts.core.stat
StatUtils - Class in bacnet.scripts.core.stat
StatUtils() - Constructor for class bacnet.scripts.core.stat.StatUtils
STDEV - Enum constant in enum bacnet.table.core.ColorMapper.TypeMapper
STDEV - Enum constant in enum bacnet.table.core.ColorMapperRCP.Type
STDEVWT - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
stop(BundleContext) - Method in class bacnet.e4.rap.setup.Activator
stop(BundleContext) - Method in class bacnet.scripts.Activator
StopCodonSequence - Class in org.biojava3.core.sequence: Used to map the stop codon sequence on a gene
StopCodonSequence(TranscriptSequence, int, int) - Constructor for class org.biojava3.core.sequence.StopCodonSequence
str - Variable in class bacnet.utils.StringColor
strand - Variable in class bacnet.scripts.blast.BlastResult
Strand - Enum in org.biojava3.core.sequence: Provides a way of representing the strand of a sequence, location hit or feature.
StringColor - Class in bacnet.utils
StringColor() - Constructor for class bacnet.utils.StringColor
StringManipulationHelper - Class in org.biojava3.core.util: A utility class for common String manipulation tasks.
StringProxySequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.loader: An example of a ProxySequenceReader that is created from a String.
StringProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.loader.StringProxySequenceReader
STYLE - Static variable in class bacnet.raprcp.NavigationManagement
SUB_SEQUENCE_DATA - Enum constant in enum org.biojava3.core.sequence.SequenceOptimizationHints.SequenceUsage
subArray(String[][], int, int) - Static method in class bacnet.utils.ArrayUtils
subArray(String[][], ArrayList<Integer>, ArrayList<Integer>) - Static method in class bacnet.utils.ArrayUtils: Return an array which correspond to the row and colum
SubCellCompartment - Class in bacnet.datamodel.annotation: All data and methods for Subcellular compartment information are done here
SubCellCompartment() - Constructor for class bacnet.datamodel.annotation.SubCellCompartment
SubCellCompartment.TypeCompartment - Enum in bacnet.datamodel.annotation
submit(Callable<T>) - Static method in class org.biojava3.core.util.ConcurrencyTools: Queues up a task and adds a default log entry.
submit(Callable<T>, String) - Static method in class org.biojava3.core.util.ConcurrencyTools: Queues up a task and adds a log entry.
Substitute(String, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Substitute
Substitute(Sequence<C>, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Substitute
subVector(double[], int, int) - Static method in class bacnet.utils.VectorUtils: Return the subVector of vector between index begin and index end
suffix(int) - Method in class org.biojava3.genome.parsers.gff.Location: The part of this location after the specified position.
suffix(Location) - Method in class org.biojava3.genome.parsers.gff.Location: The part of this location after the other location (not inclusive).
sum(double[]) - Static method in class bacnet.utils.VectorUtils: Sum of all term in the vector
sum(double[][]) - Static method in class bacnet.utils.ArrayUtils
summarize(Experiment, Genome) - Static method in class bacnet.scripts.core.Expression: Create 3 ExpressionMatrix:
GeneExpression of genes on all BioCondition, saved in PATH_ALLGENEXPR Tiling of genes on all BioCondition, saved in PATH_ALLTILING_GENE Tiling of Srnas on all BioCondition, saved in PATH_ALLTILING_SRNA
summarizeDiffExpr(Experiment, Genome) - Static method in class bacnet.scripts.database.ComparisonsCreation: Create an array :
Column = comparison Row = Gene, Srna or Asrna Cell = "+" if a specific gene has been detected over-expressed, and "-" if under-expressed

Save it in : Comparison.PATH_DIFF_LISTS+".txt"
summarizeDiffLists(Experiment) - Static method in class bacnet.scripts.database.ComparisonsCreation: Create an array :
Row = comparison Column = Number of gene, Srna Asrna over or under-expressed

Save it in : Comparison.PATH_DIFF_LISTS+".txt"
summarizeProteomes(Experiment, String) - Static method in class bacnet.scripts.database.ProteomicsCreation: Create a table will all protein expression for each Genome
summarizeResultsInTable() - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Read all the XML results of Blast and create two PhyloXML files and a sRNA conservation table
summarizeResultsInTable(ArrayList<Srna>) - Static method in class bacnet.scripts.listeriomics.srna.Srna10403SOliver: Read all the XML results of Blast and create a sRNA conservation table
header = {"Srna","EGD-e identites","EGD-e begin","EGD-e end","10403S identities","10403S begin","10403S end","10403S Average GEI","Delta_sigB Average GEI","FC range (10403S/Delta_sigB)"};
summarizeResultsInTable(ArrayList<Srna>) - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Read all the XML results of Blast and create two PhyloXML files and a sRNA conservation table
summarizeResultsInTable10403S() - Static method in class bacnet.scripts.listeriomics.srna.SrnaAlignmentBlastN: Read all the XML results of Blast and create two PhyloXML files and a sRNA conservation table
SummaryListeriomics - Class in bacnet.scripts.listeriomics: Methods for creating the different figures and Tables of the paper
SummaryListeriomics() - Constructor for class bacnet.scripts.listeriomics.SummaryListeriomics
SUPERIOR - Enum constant in enum bacnet.table.core.Filter.TypeFilter
SUPERIOR - Enum constant in enum bacnet.utils.Filter.TypeFilter
SUPERIOR_ABS - Enum constant in enum bacnet.table.core.Filter.TypeFilter
SUPERIOR_ABS - Enum constant in enum bacnet.utils.Filter.TypeFilter
SVG - Static variable in class bacnet.utils.HTMLUtils
swtColorToAwt(Color) - Static method in class bacnet.table.core.ColorMapperRCP
SWTResourceManager - Class in bacnet.swt: Utility class for managing OS resources associated with SWT controls such as colors, fonts, images, etc.
SWTResourceManager() - Constructor for class bacnet.swt.SWTResourceManager
symDifference(ArrayList<String>, ArrayList<String>) - Static method in class bacnet.utils.ListUtils: Calculate symmetrical difference of two lists L1 and L2
SynTView - Class in bacnet.e4.rap
SynTView() - Constructor for class bacnet.e4.rap.SynTView
SystemsBiologyListeriomics - Class in bacnet.scripts.listeriomics: List of method to create Co-expression network and analyse it
SystemsBiologyListeriomics() - Constructor for class bacnet.scripts.listeriomics.SystemsBiologyListeriomics

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