Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
O
- offset(int) - Method in class org.biojava3.core.sequence.location.FuzzyPoint
- offset(int) - Method in class org.biojava3.core.sequence.location.SimplePoint
- offset(int) - Method in interface org.biojava3.core.sequence.location.template.Point
-
Returns a new point offset by the given distance
- okPressed() - Method in class bacnet.expressionAtlas.core.SelectGenomeElementDialog
-
When Ok is pressed, update the different genome elements sleected
- okPressed() - Method in class bacnet.genomeBrowser.dialog.AddProteomicsDataDialog
- okPressed() - Method in class bacnet.genomeBrowser.dialog.AddTranscriptomicsDataDialog
- okPressed() - Method in class bacnet.genomeBrowser.dialog.LegendDialog
- okPressed() - Method in class bacnet.table.gui.FilterDialog
- okPressed() - Method in class bacnet.table.gui.FilterExpressionMatrixDialog
- okPressed() - Method in class bacnet.table.gui.HideExpressionMatrixDialog
- OldLocusTagArray - Static variable in class bacnet.datamodel.annotation.LocusTag
- OmicsData - Class in bacnet.datamodel.dataset
-
Abstract Class describing data related to omics data
- OmicsData() - Constructor for class bacnet.datamodel.dataset.OmicsData
- OmicsData.ColNames - Enum in bacnet.datamodel.dataset
- OmicsData.TypeData - Enum in bacnet.datamodel.dataset
-
Enum referencing the different type of OmicsData possible: GeneExpr Tiling RNASeq TSS (Transcription Initiation Site) NTerm (Translation Initiation Site) Proteome (Matrix of protein found) MassSpec (List of peptides found by mass spectrometry) ExpressionMatrix (General matrix format) unknown
- omitOverlapping(String, Location, boolean) - Method in class org.biojava3.genome.parsers.gff.FeatureList
-
Create a list of all features that do not overlap the specified location on the specified sequence.
- ONE - Enum constant in enum org.biojava3.core.sequence.transcription.Frame
- OneOfLocation(List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OneOfLocation
- OneOfLocation(Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OneOfLocation
- onFocus() - Method in class bacnet.e4.rap.InitViewBacnet
- onFocus() - Method in class bacnet.e4.rap.InitViewListeria
- onFocus() - Method in class bacnet.e4.rap.InitViewListeriaSample
- onFocus() - Method in class bacnet.e4.rap.InitViewYersinia
- onFocus() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
- onFocus() - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
- onFocus() - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
- onFocus() - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
- onFocus() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
- onFocus() - Method in class bacnet.expressionAtlas.ProteomicsView
- onFocus() - Method in class bacnet.expressionAtlas.TranscriptomicsView
- onFocus() - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
- onFocus() - Method in class bacnet.genomeBrowser.NTerminomicsView
- onFocus() - Method in class bacnet.sequenceTools.AnnotationView
- onFocus() - Method in class bacnet.sequenceTools.GeneView
- onFocus() - Method in class bacnet.sequenceTools.GenomicsView
- onFocus() - Method in class bacnet.sequenceTools.SrnaView
- onFocus() - Method in class bacnet.views.CoExprNetworkView
- open8081GeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display 8081 - open91001GeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display 91001 - openAnnotationView(EPartService, Genome) - Static method in class bacnet.sequenceTools.AnnotationView
-
Display a given gene
- OpenExpressionMatrixAndComparisons - Class in bacnet.expressionAtlas.core
-
Run thread for opening BioCondition, Comparisons, detect Genome and open corresponding LogFC ExpressionMatrix
- OpenExpressionMatrixAndComparisons(ArrayList<String>, HashMap<String, ArrayList<String>>, boolean) - Constructor for class bacnet.expressionAtlas.core.OpenExpressionMatrixAndComparisons
-
Open BioCondition, Comparisons, detect Genome and open corresponding LogFC ExpressionMatrix
- openFile(File) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
-
For a filename this code will check the extension of the file for a .gz extension.
- openGeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display Genome.getDefautGenome(); CO92 - OpenGenomesThread(ArrayList<String>) - Constructor for class bacnet.datamodel.sequence.Genome.OpenGenomesThread
- openHTML(String, String, EPartService) - Static method in class bacnet.views.InternalBrowser
-
Open an HTML file
- openIP32953GeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display IP32953 - openKIMGeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display KIM - openList(ArrayList<String>, String, EPartService) - Static method in class bacnet.views.InternalBrowser
-
Open an HTML version of the String ArrayList
- openPasswordDialog() - Method in class bacnet.e4.rap.InitViewListeriaSample
- openPasswordDialog(Shell) - Method in class bacnet.e4.rap.AppSpecificMethods
-
Push states to change url
- openPB1GeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
- openPestoidesGeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
- openQMA0440GeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display QMA0440 - openTable(String[][], String, EPartService) - Static method in class bacnet.views.InternalBrowser
-
Open an HTML version of the String array
- openTag(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
- openTag(String) - Method in interface org.biojava3.core.util.XMLWriter
-
Open a new unqualified XML tag.
- openTag(String, String) - Method in class org.biojava3.core.util.PrettyXMLWriter
- openTag(String, String) - Method in interface org.biojava3.core.util.XMLWriter
-
Open a new namespace-qualified XML tag.
- openText(String, String, EPartService) - Static method in class bacnet.views.InternalBrowser
-
Open an HTML version of the String
- openURL(String, String, EPartService) - Static method in class bacnet.views.InternalBrowser
-
Open an HTML file
- openURLInExternalBrowser(String, EPartService) - Static method in class bacnet.raprcp.NavigationManagement
-
Show the help page in an external browser
- openView(EPartService, String) - Static method in class bacnet.table.TableSWTView
-
Open a HeatMapTranscriptomicsView using EPartService and an id
- openView(EPartService, String, String) - Static method in class bacnet.swt.ResourceManager
-
Open a HeatMapTranscriptomicsView using EPartService and an id !!!!!!
- openWAGeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
- openY11GeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display Y11 - openYPIIIGeneView(EPartService) - Static method in class bacnet.sequenceTools.GeneView
-
Display GeneView
It will display YPIII - Operon - Class in bacnet.datamodel.sequence
- Operon - Enum constant in enum bacnet.datamodel.sequence.Sequence.SeqType
- Operon() - Constructor for class bacnet.datamodel.sequence.Operon
- Operon(String, int, int, char) - Constructor for class bacnet.datamodel.sequence.Operon
- operons - Variable in class bacnet.scripts.genome.CircularGenomeJPanel
- opposite() - Method in class org.biojava3.genome.parsers.gff.Location
-
Return location that is in same position on opposite strand.
- ORANGE - Static variable in class bacnet.utils.BasicColor
- OrderLocation(int, int, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
- OrderLocation(int, int, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
- OrderLocation(Point, Point, Strand, boolean, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
- OrderLocation(Point, Point, Strand, boolean, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
- OrderLocation(Point, Point, Strand, List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
- OrderLocation(Point, Point, Strand, Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.OrderLocation
- org.biojava3.core.exceptions - package org.biojava3.core.exceptions
- org.biojava3.core.sequence - package org.biojava3.core.sequence
- org.biojava3.core.sequence.compound - package org.biojava3.core.sequence.compound
- org.biojava3.core.sequence.edits - package org.biojava3.core.sequence.edits
- org.biojava3.core.sequence.features - package org.biojava3.core.sequence.features
- org.biojava3.core.sequence.io - package org.biojava3.core.sequence.io
- org.biojava3.core.sequence.io.template - package org.biojava3.core.sequence.io.template
- org.biojava3.core.sequence.io.util - package org.biojava3.core.sequence.io.util
- org.biojava3.core.sequence.loader - package org.biojava3.core.sequence.loader
- org.biojava3.core.sequence.location - package org.biojava3.core.sequence.location
- org.biojava3.core.sequence.location.template - package org.biojava3.core.sequence.location.template
- org.biojava3.core.sequence.storage - package org.biojava3.core.sequence.storage
- org.biojava3.core.sequence.template - package org.biojava3.core.sequence.template
- org.biojava3.core.sequence.transcription - package org.biojava3.core.sequence.transcription
- org.biojava3.core.sequence.views - package org.biojava3.core.sequence.views
- org.biojava3.core.util - package org.biojava3.core.util
- org.biojava3.genome - package org.biojava3.genome
- org.biojava3.genome.parsers.geneid - package org.biojava3.genome.parsers.geneid
- org.biojava3.genome.parsers.gff - package org.biojava3.genome.parsers.gff
- org.biojava3.genome.query - package org.biojava3.genome.query
- org.biojava3.genome.uniprot - package org.biojava3.genome.uniprot
- org.biojava3.genome.util - package org.biojava3.genome.util
- organizePhyloTable(String) - Static method in class bacnet.scripts.database.PhylogenomicsCreation
- organizeResults(String) - Static method in class bacnet.scripts.genome.SDProfile
-
Go through the tables created, reorganize the different indexes to order Base pairs.
For random values, verify that the SD calculation is good. - OTHER - Enum constant in enum bacnet.table.core.ColorMapper.TypeMapper
- OTHER - Enum constant in enum bacnet.table.core.ColorMapperRCP.Type
- outerProduct(double[][]) - Static method in class bacnet.utils.ArrayUtils
-
Calcul of the Outer Product Matrix
- outputFastaSequenceLengthGFF3(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
-
Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file.
- OutputHitsGFF - Class in org.biojava3.genome.query
- OutputHitsGFF() - Constructor for class org.biojava3.genome.query.OutputHitsGFF
- outputName - Static variable in class bacnet.scripts.blast.BlastOutput
- outputToStream(Document, OutputStream) - Static method in class org.biojava3.core.util.XMLHelper
- outputToStream(Element, OutputStream) - Static method in class org.biojava3.core.util.XMLHelper
- overlap(Sequence, Sequence) - Static method in class bacnet.datamodel.sequence.Sequence
-
Calculate the overlapping size of two genes
First, find the gene upstream to the other
Then, as we got gene1.begin < gene2.begin, overlap = gene1.end - gene2.begin
overlap can be negative, it will mean that we have no overlap (gene1.end < gene2.begin)
or overlap can be higher than gene2.length, in that case overlap = gene2.length - overlap(DNASequence, DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
-
Calculate the overlapping size of two genes
First, find the gene upstream to the other
Then, as we got gene1.begin < gene2.begin, overlap = gene1.end - gene2.begin
overlap can be negative, it will mean that we have no overlap (gene1.end < gene2.begin)
or overlap can be higher than gene2.length, in that case overlap = gene2.length - overlapEqual(int[], double) - Static method in class bacnet.datamodel.proteomics.NTermFilter
-
Return true if overlap[0] < value
- overlapInf(int[], double) - Static method in class bacnet.datamodel.proteomics.NTermFilter
-
Return true if overlap[0] < value
- overlappingKmers(Sequence<C>, int) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
Used to generate overlapping k-mers such i.e.
- overlaps(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Check if this location and other location overlap.
- overlapSup(int[], double) - Static method in class bacnet.datamodel.proteomics.NTermFilter
-
Return true if overlap[0] < value
- OVERLAY - Enum constant in enum bacnet.genomeBrowser.core.Track.DisplayType
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