Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
I
- iCM - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
- ID - Static variable in class bacnet.e4.rap.BannerView
- ID - Static variable in class bacnet.e4.rap.InitViewBacnet
- ID - Static variable in class bacnet.e4.rap.InitViewListeria
- ID - Static variable in class bacnet.e4.rap.InitViewListeriaSample
- ID - Static variable in class bacnet.e4.rap.InitViewYersinia
- ID - Static variable in class bacnet.e4.rap.SynTView
- ID - Static variable in class bacnet.expressionAtlas.HeatMapMultiOmicsView
- ID - Static variable in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
- ID - Static variable in class bacnet.expressionAtlas.HeatMapProteomicsView
- ID - Static variable in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
- ID - Static variable in class bacnet.expressionAtlas.ProteomicsExpressionView
- ID - Static variable in class bacnet.expressionAtlas.ProteomicsView
- ID - Static variable in class bacnet.expressionAtlas.TranscriptomicsView
- ID - Static variable in class bacnet.genomeBrowser.GenomeTranscriptomeView
- ID - Static variable in class bacnet.genomeBrowser.NTerminomicsView
- ID - Static variable in class bacnet.sequenceTools.AnnotationView
- ID - Static variable in class bacnet.sequenceTools.GeneView
- ID - Static variable in class bacnet.sequenceTools.GenomicsView
- ID - Static variable in class bacnet.sequenceTools.SrnaSummaryView
- ID - Static variable in class bacnet.sequenceTools.SrnaView
- ID - Static variable in class bacnet.table.TableSWTView
- ID - Static variable in class bacnet.views.BannerView
- ID - Static variable in class bacnet.views.CoExprNetworkView
- ID - Static variable in class bacnet.views.CRISPRPredictView
- ID - Static variable in class bacnet.views.CRISPRPredictView2
- ID - Static variable in class bacnet.views.InitView
- ID - Static variable in class bacnet.views.InternalBrowser
- ident - Variable in class bacnet.scripts.blast.BlastResult
- identities - Variable in class bacnet.scripts.blast.BlastResult
- IDENTITY_CUTOFF - Static variable in class bacnet.scripts.database.HomologCreation
-
Cutoff for indeityt value
- IHM - Class in bacnet.scripts.listeriomics.technology
- IHM() - Constructor for class bacnet.scripts.listeriomics.technology.IHM
- ImageMagick - Class in bacnet.utils
-
Methods link to image mlanipulation with ImageMagick
- ImageMagick() - Constructor for class bacnet.utils.ImageMagick
- indexOf(Sequence<C>, C) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
Performs a linear search of the given Sequence for the given compound.
- INFERIOR - Enum constant in enum bacnet.table.core.Filter.TypeFilter
- INFERIOR - Enum constant in enum bacnet.utils.Filter.TypeFilter
- INFERIOR_ABS - Enum constant in enum bacnet.table.core.Filter.TypeFilter
- INFERIOR_ABS - Enum constant in enum bacnet.utils.Filter.TypeFilter
- initBacnetApp(EPartService, EModelService, Shell) - Static method in class bacnet.e4.rap.SessionControl
-
Performed all initialisation necessary at the running of the webapp
Is runned in BannerView.createPartControl() - initBacnetApp(EPartService, EModelService, Shell) - Static method in class bacnet.e4.rap.setup.SessionControl
-
Performed all initialisation necessary at the running of the webapp
Is runned in BannerView.createPartControl() - initComboGenome() - Method in class bacnet.views.CoExprNetworkView
- initData(ExpressionMatrix) - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
-
Init data and filter lists
- initData(ExpressionMatrix, Genome) - Method in class bacnet.table.TableSWTComposite
-
Init data and filter lists
- initDatabase(String) - Static method in class bacnet.Database
-
Initialize appropriate database with right files
- initDatabase(Shell) - Method in class bacnet.Database
-
Run at the initialization of the workbench in Eclipse RAP website
- initDatabaseMonitor(Database, IProgressMonitor) - Static method in class bacnet.Database
-
Initialize appropriate database with right files
- InitDatabaseThread(Database) - Constructor for class bacnet.Database.InitDatabaseThread
- initDisplay() - Method in class bacnet.table.gui.FilterDialog
- initDisplayBoolean() - Method in class bacnet.genomeBrowser.core.DataTrack
-
Initiate Display boolean Vector when the first is added
- initMet(boolean) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
- InitNetworkThread(CoExprNetworkView) - Constructor for class bacnet.views.CoExprNetworkView.InitNetworkThread
- InitOmicsMatrixThread(HeatMapMultiOmicsView) - Constructor for class bacnet.expressionAtlas.HeatMapMultiOmicsView.InitOmicsMatrixThread
- initStaticVariables() - Static method in class bacnet.datamodel.dataset.OmicsData
-
Reinit static variables of OmicsData when database path is changed
- initStaticVariables() - Static method in class bacnet.datamodel.phylogeny.Phylogenomic
-
Init static variables after Database change
- initStaticVariables() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Init static variables after Database change
- initView() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
- InitView - Class in bacnet.views
- InitView() - Constructor for class bacnet.views.InitView
- InitViewBacnet - Class in bacnet.e4.rap
- InitViewBacnet() - Constructor for class bacnet.e4.rap.InitViewBacnet
- InitViewListeria - Class in bacnet.e4.rap
- InitViewListeria() - Constructor for class bacnet.e4.rap.InitViewListeria
- InitViewListeriaSample - Class in bacnet.e4.rap
- InitViewListeriaSample() - Constructor for class bacnet.e4.rap.InitViewListeriaSample
- InitViewYersinia - Class in bacnet.e4.rap
- InitViewYersinia() - Constructor for class bacnet.e4.rap.InitViewYersinia
- innerProduct(double[][]) - Static method in class bacnet.utils.ArrayUtils
-
Calcul of the Inner Product Matrix
- InputStreamProvider - Class in org.biojava3.core.util
-
A class that provides an InputStream from a File.
- InputStreamProvider() - Constructor for class org.biojava3.core.util.InputStreamProvider
- inputStreamToDocument(InputStream) - Static method in class org.biojava3.core.util.XMLHelper
- InsdcLocations - Class in org.biojava3.core.sequence.location
-
A collection of locations which are used whenever we work with INSDC; some of which could be deprecated (from INSDC's point of view) yet appear in records.
- InsdcLocations() - Constructor for class org.biojava3.core.sequence.location.InsdcLocations
- InsdcLocations.BondLocation - Class in org.biojava3.core.sequence.location
-
Used to represent bond locations equivalent to bond(7,8) or bond(7).
- InsdcLocations.GroupLocation - Class in org.biojava3.core.sequence.location
-
Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined.
- InsdcLocations.OneOfLocation - Class in org.biojava3.core.sequence.location
-
Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g.
- InsdcLocations.OrderLocation - Class in org.biojava3.core.sequence.location
-
Used to describe a 5' to 3' ordering but no firm assurance it is correct
- InsdcParser - Class in org.biojava3.core.sequence.location
-
Parser for working with INSDC style locations.
- InsdcParser() - Constructor for class org.biojava3.core.sequence.location.InsdcParser
- InsdcParser(DataSource) - Constructor for class org.biojava3.core.sequence.location.InsdcParser
- Insert(String, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
- Insert(String, int, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
- Insert(Sequence<C>, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
- Insert(Sequence<C>, int, int) - Constructor for class org.biojava3.core.sequence.edits.Edit.Insert
- InternalBrowser - Class in bacnet.views
- InternalBrowser() - Constructor for class bacnet.views.InternalBrowser
- intersect(String[], String[]) - Static method in class bacnet.utils.VectorUtils
-
Calculate intersection of two vectors L1 and L2
- intersect(ArrayList<String[]>) - Static method in class bacnet.utils.VectorUtils
-
Calculate the intersection of a list of Vector
- intersect(ArrayList<String>, ArrayList<String>) - Static method in class bacnet.utils.ListUtils
-
Calculate intersection of two lists L1 and L2
- intersect(ArrayList<ArrayList<String>>) - Static method in class bacnet.utils.ListUtils
-
Calculate the intersection of a list of lists
- intersection(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Return the intersection, or null if no overlap.
- IntronSequence - Class in org.biojava3.core.sequence
- IntronSequence(GeneSequence, int, int) - Constructor for class org.biojava3.core.sequence.IntronSequence
-
Place holder for Intron sequence features
- intValue() - Method in class org.biojava3.core.sequence.transcription.Table.CaseInsensitiveTriplet
-
Attempts to provide an int version of this codon which multiplies each position by
- inverse(ArrayList<String>, ArrayList<String>) - Static method in class bacnet.utils.ListUtils
-
Return the invert list of List1 inside the total universe
- inverse(Sequence<C>) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
-
A method which attempts to do the right thing when is comes to a reverse/reverse complement
- IOUtils - Class in org.biojava3.core.sequence.io.util
- IOUtils() - Constructor for class org.biojava3.core.sequence.io.util.IOUtils
- IOUtils.ReaderProcessor - Interface in org.biojava3.core.sequence.io.util
-
Closure interface used when working with
IOUtils#processReader(String). - isAfter(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Check if this location is entirely after the other location (no overlap).
- isAlreadyRead() - Method in class bacnet.datamodel.dataset.ExpressionData
- isAmbiguous() - Method in class org.biojava3.core.sequence.compound.NucleotideCompound
- isBefore(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Check if this location is entirely before other location (no overlap).
- isBetweenCompounds() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
- isBetweenCompounds() - Method in interface org.biojava3.core.sequence.location.template.Location
-
Returns true if the position is meant to represent a point between two points such as 78^79.
- isCircular() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
- isCircular() - Method in interface org.biojava3.core.sequence.location.template.Location
-
Indicates if this location is circular.
- isComplementable() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
- isComplementable() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
- isComplementable() - Method in class org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet
-
NucleotideCompounds can always complement
- isComplementable() - Method in interface org.biojava3.core.sequence.template.CompoundSet
- isCompleteGenome(String) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
-
Detect if the genome is a Complete genome or a WGS using DATABASES_LIST_PATH table
- isComplex() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
- isComplex() - Method in interface org.biojava3.core.sequence.location.template.Location
-
Returns true if the location is considered to be complex meaning the location is actually composed of sub-locations.
- isCompoundStringLengthEqual() - Method in class org.biojava3.core.sequence.compound.AminoAcidCompoundSet
- isCompoundStringLengthEqual() - Method in class org.biojava3.core.sequence.template.AbstractCompoundSet
- isCompoundStringLengthEqual() - Method in interface org.biojava3.core.sequence.template.CompoundSet
-
Returns true if all String representations of Compounds are of the same length.
- isDataRead() - Method in class bacnet.datamodel.dataset.GeneExpression
- isDisplayAbsoluteValue() - Method in class bacnet.genomeBrowser.core.DataTrack
- isDisplayMouseLine() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
- isDisplayMouseLine() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome
- isDisplaySequence() - Method in class bacnet.genomeBrowser.core.Track
- isEqual(Sequence) - Method in class bacnet.datamodel.sequence.Sequence
-
If : sequence.getBegin()==this.getBegin() && sequence.getEnd()==this.getEnd() && sequence.getStrand()==this.getStrand()
return true - isEqual(Srna, int) - Method in class bacnet.datamodel.sequence.Srna
- isEqual(DNASequence, DNASequence, int) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
-
Calculates the distance between the two center fo gene1 and gene2
If this distance is under scale, in absolute value, and both gene are on the same strand, True is return - isFilterColumn() - Method in class bacnet.table.core.Filter
- isFilterColumn() - Method in class bacnet.utils.Filter
- isFocused() - Method in class bacnet.e4.rap.InitViewBacnet
- isFocused() - Method in class bacnet.e4.rap.InitViewListeria
- isFocused() - Method in class bacnet.e4.rap.InitViewListeriaSample
- isFocused() - Method in class bacnet.e4.rap.InitViewYersinia
- isFocused() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
- isFocused() - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView
- isFocused() - Method in class bacnet.expressionAtlas.HeatMapProteomicsView
- isFocused() - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView
- isFocused() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView
- isFocused() - Method in class bacnet.expressionAtlas.ProteomicsView
- isFocused() - Method in class bacnet.expressionAtlas.TranscriptomicsView
- isFocused() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
- isFocused() - Method in class bacnet.sequenceTools.AnnotationView
- isFocused() - Method in class bacnet.sequenceTools.GeneView
- isFocused() - Method in class bacnet.sequenceTools.GenomicsView
- isFocused() - Method in class bacnet.sequenceTools.SrnaView
- isFocused() - Method in class bacnet.views.CoExprNetworkView
- isForMandAltStart(NTerm) - Static method in class bacnet.datamodel.proteomics.NTermFilter
-
Find if the NTerm start with a Methyonine
if it corresponds to a regular start codon "ATG" we need a Formyl modificaition to prove its a real translation initiation
If the methyonine corresponds to any other type of start codon, we don't need more to prove it's a translation initiation - isFormylated() - Method in class bacnet.datamodel.proteomics.TIS
-
Return true if the TIS includes a formylated NTerm
- isHigher(Point) - Method in class org.biojava3.core.sequence.location.SimplePoint
- isHigher(Point) - Method in interface org.biojava3.core.sequence.location.template.Point
-
Returns true if the point is higher in value to the current point
- isInfoRead() - Method in class bacnet.datamodel.dataset.ExpressionData
- isInfoRead() - Method in class bacnet.datamodel.dataset.NGS
- isInitialized() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
- isInsoluble() - Method in class bacnet.datamodel.proteomics.NTerm
- isInteger(double) - Static method in class bacnet.utils.MathUtils
-
Test if a double is an integer or not
- isIntersect() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView
- isLoaded() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
- isLogTransformed() - Method in class bacnet.datamodel.dataset.NGS
- isLower(Point) - Method in class org.biojava3.core.sequence.location.SimplePoint
- isLower(Point) - Method in interface org.biojava3.core.sequence.location.template.Point
-
Returns true if the current point is at a lower position than the point given.
- isNegative() - Method in class org.biojava3.genome.parsers.gff.Location
-
Check if location is on negative strand.
- isNGS() - Method in class bacnet.datamodel.dataset.ExpressionData
- isNoData() - Method in class bacnet.datamodel.expdesign.BioCondition
- isNucleotide() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
- isNucleotideSequence(String) - Static method in class org.biojava3.core.util.SequenceTools
- isOrdered() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
- isOverlap(Sequence, Sequence) - Static method in class bacnet.datamodel.sequence.Sequence
-
Decide if two genes are overlapping
First, calculate the overlapping size of two genes, finding the gene upstream to the other
If overlap is negative it will mean that we have no overlap (gene1.end < gene2.begin) - isOverlap(Sequence, Sequence, int) - Static method in class bacnet.datamodel.sequence.Sequence
-
Decide if two genes are overlapping
First, calculate the overlapping size of two genes, finding the gene upstream to the other
If overlap is negative it will mean that we have no overlap (gene1.end < gene2.begin) - isOverlap(DNASequence, DNASequence) - Static method in class bacnet.datamodel.sequenceNCBI.GeneNCBITools
-
Decide if two genes are overlapping
First, calculate the overlapping size of two genes, finding the gene upstream to the other
If overlap is negative it will mean that we have no overlap (gene1.end < gene2.begin) - isOverlapInFrame() - Method in class bacnet.datamodel.proteomics.NTerm
- isOverlapStart(Sequence, Sequence, int) - Static method in class bacnet.datamodel.sequence.Sequence
-
Decide if first Sequence is overlapping the start region of the second
- isPseudogene() - Method in class bacnet.datamodel.sequence.Gene
- isSameStrand(Sequence, Sequence) - Static method in class bacnet.datamodel.sequence.Sequence
-
Decide if two sequences have same strand
- isSameStrand(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Check if this location is on same strand as other location.
- isSoluble() - Method in class bacnet.datamodel.proteomics.NTerm
- isStart() - Method in class org.biojava3.core.sequence.compound.CodonCompound
- isStart() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
- isStart(NTerm, String) - Static method in class bacnet.datamodel.proteomics.NTermFilter
-
Find i an NTerm start with a methyonine (START), or if the amino acid just before the peptide is a Methyonine (START-1), or just after (START+1)
- isStart(String) - Static method in class bacnet.datamodel.sequence.Codon
-
Test if a codon is a start codon
- isStart(AminoAcidCompound) - Method in class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
-
Returns true if the given compound was a start codon in this codon table.
- isStart(AminoAcidCompound) - Method in interface org.biojava3.core.sequence.transcription.Table
-
Returns true if the given compound could have been a start amino acid; this does not assert if the codon that actually coded for the amino acid was a start codon.
- isStop() - Method in class org.biojava3.core.sequence.transcription.Table.Codon
- isStop(String) - Static method in class bacnet.datamodel.sequence.Codon
-
Test if a codon is a stop codon
- isStrand() - Method in class bacnet.datamodel.sequence.Sequence
-
Return True if strand=='+'
- isTestData() - Method in class bacnet.genomeBrowser.tracksGUI.TrackCanvasData
- isTiling() - Method in class bacnet.scripts.core.Comparison
- isTranscriptomics() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap
- isUncertain() - Method in class org.biojava3.core.sequence.location.SimplePoint
- isUncertain() - Method in interface org.biojava3.core.sequence.location.template.Point
-
Returns a true if the exact point is unknown.
- isUnknown() - Method in class org.biojava3.core.sequence.location.SimplePoint
- isUnknown() - Method in interface org.biojava3.core.sequence.location.template.Point
-
Returns true if the current position is unknown but is beyond the position encoded for.
- isWildType() - Method in class bacnet.datamodel.expdesign.BioCondition
- isZoomChangedFlag() - Method in class bacnet.genomeBrowser.core.Zoom
- ITEM - Static variable in class bacnet.raprcp.NavigationManagement
- iterator() - Method in class org.biojava3.core.sequence.loader.SequenceFileProxyLoader
- iterator() - Method in class org.biojava3.core.sequence.loader.StringProxySequenceReader
- iterator() - Method in class org.biojava3.core.sequence.loader.UniprotProxySequenceReader
- iterator() - Method in class org.biojava3.core.sequence.location.template.AbstractLocation
-
Iterates through all known sub-locations for this location but does not descend
- iterator() - Method in class org.biojava3.core.sequence.storage.ArrayListSequenceReader
- iterator() - Method in class org.biojava3.core.sequence.storage.BitSequenceReader
-
Provides basic iterable access to this class
- iterator() - Method in class org.biojava3.core.sequence.storage.JoiningSequenceReader
-
Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
- iterator() - Method in class org.biojava3.core.sequence.storage.SingleCompoundSequenceReader
-
Returns an instance of
SequenceMixin.SequenceIterator - iterator() - Method in class org.biojava3.core.sequence.template.AbstractSequence
- iterator() - Method in class org.biojava3.core.sequence.template.SequenceProxyView
- iterator() - Method in class org.biojava3.core.sequence.views.WindowedSequence
-
Returns an iterator which will return the windows in a sequence in sequential order.
- iterator() - Method in class org.biojava3.genome.parsers.gff.Location
-
Create a location iterator over this location with a window size of 1 and an increment of +1 (successive symbols from start to end).
- iterator(int, int) - Method in class org.biojava3.genome.parsers.gff.Location
-
Create a location iterator over this location, using specified window size and increment.
- IUPAC_LOCATION - Static variable in class org.biojava3.core.sequence.io.IUPACParser
- IUPACParser - Class in org.biojava3.core.sequence.io
-
Available translations 1 - UNIVERSAL 2 - VERTEBRATE_MITOCHONDRIAL 3 - YEAST_MITOCHONDRIAL 4 - MOLD_MITOCHONDRIAL 5 - INVERTEBRATE_MITOCHONDRIAL 6 - CILIATE_NUCLEAR 9 - ECHINODERM_MITOCHONDRIAL 10 - EUPLOTID_NUCLEAR 11 - BACTERIAL 12 - ALTERNATIVE_YEAST_NUCLEAR 13 - ASCIDIAN_MITOCHONDRIAL 14 - FLATWORM_MITOCHONDRIAL 15 - BLEPHARISMA_MACRONUCLEAR 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL 21 - TREMATODE_MITOCHONDRIAL 23 - SCENEDESMUS_MITOCHONDRIAL Taken from NCBI with slight modification and put into the classpath resource.
- IUPACParser() - Constructor for class org.biojava3.core.sequence.io.IUPACParser
-
Default version and uses the classpath based IUPAC table
- IUPACParser(InputStream) - Constructor for class org.biojava3.core.sequence.io.IUPACParser
-
Allows you to specify a different IUPAC table.
- IUPACParser.IUPACTable - Class in org.biojava3.core.sequence.io
-
Holds the concept of a codon table from the IUPAC format
- IUPACTable(String, int, String, String, String, String, String) - Constructor for class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
- IUPACTable(String, Integer, String, String) - Constructor for class org.biojava3.core.sequence.io.IUPACParser.IUPACTable
-
Constructor which uses the basic IUPAC codon table format.
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