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

B

Bacili_NWK - Static variable in class bacnet.scripts.phylogeny.PhylogenyToolsJolley

BACNET - Static variable in class bacnet.Database

Static variable to discriminate BACNET project from the others

bacnet.datamodel.annotation - package bacnet.datamodel.annotation

bacnet.datamodel.dataset - package bacnet.datamodel.dataset

bacnet.datamodel.expdesign - package bacnet.datamodel.expdesign

bacnet.datamodel.phylogeny - package bacnet.datamodel.phylogeny

bacnet.datamodel.proteomics - package bacnet.datamodel.proteomics

bacnet.datamodel.sequence - package bacnet.datamodel.sequence

bacnet.datamodel.sequenceNCBI - package bacnet.datamodel.sequenceNCBI

bacnet.e4.rap.setup - package bacnet.e4.rap.setup

bacnet.expressionAtlas - package bacnet.expressionAtlas

bacnet.expressionAtlas.core - package bacnet.expressionAtlas.core

bacnet.genomeBrowser - package bacnet.genomeBrowser

bacnet.genomeBrowser.core - package bacnet.genomeBrowser.core

bacnet.genomeBrowser.dialog - package bacnet.genomeBrowser.dialog

bacnet.genomeBrowser.tracksGUI - package bacnet.genomeBrowser.tracksGUI

bacnet.handler - package bacnet.handler

bacnet.raprcp - package bacnet.raprcp

bacnet.reader - package bacnet.reader

bacnet.scripts - package bacnet.scripts

bacnet.scripts.arrayexpress - package bacnet.scripts.arrayexpress

bacnet.scripts.blast - package bacnet.scripts.blast

bacnet.scripts.core - package bacnet.scripts.core

bacnet.scripts.core.normalization - package bacnet.scripts.core.normalization

bacnet.scripts.core.stat - package bacnet.scripts.core.stat

bacnet.scripts.core.vennDiagram - package bacnet.scripts.core.vennDiagram

bacnet.scripts.database - package bacnet.scripts.database

bacnet.scripts.genome - package bacnet.scripts.genome

bacnet.scripts.listeriomics - package bacnet.scripts.listeriomics

bacnet.scripts.listeriomics.ArrayExpress - package bacnet.scripts.listeriomics.ArrayExpress

bacnet.scripts.listeriomics.nterm - package bacnet.scripts.listeriomics.nterm

bacnet.scripts.listeriomics.srna - package bacnet.scripts.listeriomics.srna

bacnet.scripts.listeriomics.technology - package bacnet.scripts.listeriomics.technology

bacnet.scripts.phylogeny - package bacnet.scripts.phylogeny

bacnet.sequenceTools - package bacnet.sequenceTools

bacnet.swt - package bacnet.swt

bacnet.table - package bacnet.table

bacnet.table.core - package bacnet.table.core

bacnet.table.gui - package bacnet.table.gui

bacnet.utils - package bacnet.utils

bacnet.views - package bacnet.views

BacnetE4PointFactory - Class in bacnet.e4.rap

BacnetE4PointFactory - Class in bacnet.e4.rap.setup

BacnetE4PointFactory(E4ApplicationConfig) - Constructor for class bacnet.e4.rap.BacnetE4PointFactory

BacnetE4PointFactory(E4ApplicationConfig) - Constructor for class bacnet.e4.rap.setup.BacnetE4PointFactory

BACSUBTILIS_NAME - Static variable in class bacnet.datamodel.sequence.Genome

Name for bacillus genome

BANNER_BACKGROUND - Static variable in class bacnet.utils.BasicColor

Very light color for the background of the software banner

BANNER_COLOR - Static variable in class bacnet.utils.BasicColor

BannerView - Class in bacnet.e4.rap

BannerView - Class in bacnet.views

BannerView() - Constructor for class bacnet.e4.rap.BannerView

BannerView() - Constructor for class bacnet.views.BannerView

BasicApplication - Class in bacnet.e4.rap

BasicApplication - Class in bacnet.e4.rap.setup

BasicApplication() - Constructor for class bacnet.e4.rap.BasicApplication

BasicApplication() - Constructor for class bacnet.e4.rap.setup.BasicApplication

BasicColor - Class in bacnet.utils

BasicColor() - Constructor for class bacnet.utils.BasicColor

BasicSequence<C extends Compound> - Class in org.biojava3.core.sequence

Bare bones version of the Sequence object to be used sparingly.

BasicSequence(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.BasicSequence

BasicSequence(ProxySequenceReader<C>) - Constructor for class org.biojava3.core.sequence.BasicSequence

begin - Variable in class bacnet.scripts.blast.BlastResult

beginQuery - Variable in class bacnet.scripts.blast.BlastResult

BETWEEN - Enum constant in enum bacnet.table.core.Filter.TypeFilter

BETWEEN - Enum constant in enum bacnet.utils.Filter.TypeFilter

bigDataset - Static variable in class bacnet.scripts.listeriomics.PhylogenyListeriomics

BIOCOND - Enum constant in enum bacnet.genomeBrowser.core.Track.DisplayType

BioCondition - Class in bacnet.datamodel.expdesign

This class is used for the different bioconds declared in the experiment It contains the biocond name, and all the related data.

BioCondition() - Constructor for class bacnet.datamodel.expdesign.BioCondition

BioCondition(String) - Constructor for class bacnet.datamodel.expdesign.BioCondition

BioConditionComparator - Class in bacnet.table.core

BioConditionComparator(ArrayList<String>) - Constructor for class bacnet.table.core.BioConditionComparator

BioConditionCreation - Class in bacnet.scripts.database

BioConditionCreation() - Constructor for class bacnet.scripts.database.BioConditionCreation

bioEnd() - Method in class org.biojava3.genome.parsers.gff.Location

Get end index, in biocoordinates.

bioStart() - Method in class org.biojava3.genome.parsers.gff.Location

Get start index, in biocoordinates.

bioStrand() - Method in class org.biojava3.genome.parsers.gff.Location

Get character representation of strand.

BitArrayWorker(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker

BitArrayWorker(CompoundSet<C>, int) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker

BitArrayWorker(CompoundSet<C>, int[]) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker

BitArrayWorker(Sequence<C>) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker

bitScore - Variable in class bacnet.scripts.blast.BlastResult

BitSequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.storage

An implementation of the popular bit encodings.

BitSequenceReader(BitSequenceReader.BitArrayWorker<C>, AccessionID) - Constructor for class org.biojava3.core.sequence.storage.BitSequenceReader

Instance which allows you to supply a different @{BitArrayWorker} object.

BitSequenceReader.BitArrayWorker<C extends Compound> - Class in org.biojava3.core.sequence.storage

The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code.

BLACK - Static variable in class bacnet.utils.BasicColor

Blast - Class in bacnet.scripts.blast

Blast() - Constructor for class bacnet.scripts.blast.Blast

blast_formatter - Static variable in class bacnet.scripts.blast.Blast

BLAST_SCRIPT_TEMP - Static variable in class bacnet.scripts.database.HomologCreation

BlastDatabase - Class in bacnet.scripts.blast

Different methods to create blast database for the genome, the ORF, and the smallORF

BlastDatabase() - Constructor for class bacnet.scripts.blast.BlastDatabase

blastdb_aliastool - Static variable in class bacnet.scripts.blast.Blast

blastdbcmd - Static variable in class bacnet.scripts.blast.Blast

blastN - Static variable in class bacnet.scripts.blast.Blast

BLASTN - Static variable in class bacnet.utils.HTMLUtils

blastNucleotide() - Static method in class bacnet.scripts.blast.Blast

BlastOutput - Class in bacnet.scripts.blast

BlastOutput() - Constructor for class bacnet.scripts.blast.BlastOutput

BlastOutput.BlastOutputTYPE - Enum in bacnet.scripts.blast

blastP - Static variable in class bacnet.scripts.blast.Blast

blastP - Static variable in class bacnet.scripts.database.HomologCreation

Shortcut for running blastP

BLASTP - Static variable in class bacnet.utils.HTMLUtils

BlastResult - Class in bacnet.scripts.blast

BlastResult(Element) - Constructor for class bacnet.scripts.blast.BlastResult

BlastResult.BlastResultCompare - Class in bacnet.scripts.blast

This comparator classify the BlastResult by their position on the genome

BlastResultCompare() - Constructor for class bacnet.scripts.blast.BlastResult.BlastResultCompare

blastX - Static variable in class bacnet.scripts.blast.Blast

BlastXMLQuery - Class in org.biojava3.genome.query

BlastXMLQuery(String) - Constructor for class org.biojava3.genome.query.BlastXMLQuery

BLUE - Static variable in class bacnet.utils.BasicColor

BLUEDARK_GENE - Static variable in class bacnet.utils.BasicColor

Dark blue color used for plus strand genes

BLUELIGHT_GENE - Static variable in class bacnet.utils.BasicColor

Light blue color used for plus strand genes

BLUELIGHT_NUCLEOTIDE - Static variable in class bacnet.utils.BasicColor

blue light color for nucleotide representation

BLUELINE_GENE - Static variable in class bacnet.utils.BasicColor

Very dark blue color used for plus strand genes surrounding

BondLocation(List<Location>) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.BondLocation

BondLocation(Location...) - Constructor for class org.biojava3.core.sequence.location.InsdcLocations.BondLocation

BOOTSTRAP - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat

BOTTOM_LEFT - Static variable in class bacnet.swt.SWTResourceManager

Style constant for placing decorator image in bottom left corner of base image.

BOTTOM_RIGHT - Static variable in class bacnet.swt.SWTResourceManager

Style constant for placing decorator image in bottom right corner of base image.

bounds() - Method in class org.biojava3.genome.parsers.gff.FeatureList

The union of all locations of all features in this list, mapped to the positive strand.

BROWN - Static variable in class bacnet.utils.BasicColor

BufferedReaderBytesRead - Class in org.biojava3.core.sequence.io

Need to keep track of actual bytes read and take advantage of buffered reader performance.

BufferedReaderBytesRead(Reader) - Constructor for class org.biojava3.core.sequence.io.BufferedReaderBytesRead

Creates a buffering character-input stream that uses a default-sized input buffer.

BufferedReaderBytesRead(Reader, int) - Constructor for class org.biojava3.core.sequence.io.BufferedReaderBytesRead

Creates a buffering character-input stream that uses an input buffer of the specified size.

build() - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder

The method to finish any calls to the builder with which returns a transcription engine.

Builder() - Constructor for class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder

buildFeatureAtrributeIndex(String, FeatureList) - Static method in class org.biojava3.genome.parsers.gff.FeatureHelper

Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files The index for the returned HashMap is the value of the attribute used to build the index

bundleChanged(BundleEvent) - Method in class bacnet.e4.rap.setup.Activator

bundleChanged(BundleEvent) - Method in class bacnet.scripts.Activator

BUTTON - Static variable in class bacnet.raprcp.NavigationManagement

BYTES_PER_INT - Static variable in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker

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