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L

Lactobacillales_NWK - Static variable in class bacnet.scripts.phylogeny.PhylogenyToolsJolley
 
lastIndexOf(Sequence<C>, C) - Static method in class org.biojava3.core.sequence.template.SequenceMixin
Performs a reversed linear search of the given Sequence by wrapping it in a ReversedSequenceView and passing it into SequenceMixin.indexOf(Sequence, Compound).
LegendDialog - Class in bacnet.genomeBrowser.dialog
 
LegendDialog(Shell, Track) - Constructor for class bacnet.genomeBrowser.dialog.LegendDialog
Create the dialog.
LEISHOMICS_PROJECT - Static variable in class bacnet.Database
Static variable to discriminate Listeriomics project from the others
length() - Method in class org.biojava3.genome.parsers.gff.Location
Get length of range.
LENGTH - Static variable in class org.biojava3.core.sequence.features.AbstractFeature
Sort features by length.
LENGTH_CUTOFF - Static variable in class bacnet.scripts.blast.ProteinTools
 
LENGTH_CUTOFF - Static variable in class bacnet.scripts.listeriomics.nterm.NTermDatabase
 
LIGHT_ASRNA - Static variable in class bacnet.utils.BasicColor
Light color used for ASrna
LIGHT_CISREG - Static variable in class bacnet.utils.BasicColor
Light color used for NCrna
LIGHT_NCRNA - Static variable in class bacnet.utils.BasicColor
Light color used for NCrna
LIGHT_ONE - Static variable in class bacnet.utils.BasicColor
 
LIGHT_OPERON - Static variable in class bacnet.utils.BasicColor
Light color used for ASrna
LIGHT_SRNA - Static variable in class bacnet.utils.BasicColor
Light color used for Srna
LIGHT_THREE - Static variable in class bacnet.utils.BasicColor
 
LIGHT_TWO - Static variable in class bacnet.utils.BasicColor
 
LIGHTBLUE - Static variable in class bacnet.utils.BasicColor
 
LIGHTERGREY - Static variable in class bacnet.utils.BasicColor
 
LIGHTGREY - Static variable in class bacnet.utils.BasicColor
 
LightweightProfile<S extends Sequence<C>,C extends Compound> - Interface in org.biojava3.core.sequence.template
Defines a minimal data structure for reading and writing a sequence alignment.
LightweightProfile.StringFormat - Enum in org.biojava3.core.sequence.template
List of output formats.
LINE_ASRNA - Static variable in class bacnet.utils.BasicColor
Very dark color used for ASrna surrounding
LINE_CISREG - Static variable in class bacnet.utils.BasicColor
Very dark color used for NCrna surrounding
LINE_NCRNA - Static variable in class bacnet.utils.BasicColor
Very dark color used for NCrna surrounding
LINE_OPERON - Static variable in class bacnet.utils.BasicColor
Very dark color used for NCrna surrounding
LINE_SRNA - Static variable in class bacnet.utils.BasicColor
Very dark color used for Srna surrounding
LIST - Static variable in class bacnet.raprcp.NavigationManagement
 
LIST_PATH - Static variable in class bacnet.scripts.arrayexpress.ArrayExpressTechnology
 
LIST_PATH - Static variable in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology
 
listAddColumn - Variable in class bacnet.table.gui.HideExpressionMatrixDialog
 
listAddRow - Variable in class bacnet.table.gui.HideExpressionMatrixDialog
 
listAllDB(String) - Static method in class bacnet.scripts.blast.Blast
 
LISTERIOMICS_PROJECT - Static variable in class bacnet.Database
Static variable to discriminate Listeriomics project from the others
listHideColumn - Variable in class bacnet.table.gui.HideExpressionMatrixDialog
 
listHideRow - Variable in class bacnet.table.gui.HideExpressionMatrixDialog
 
LISTNOTINCLUDE - Static variable in class bacnet.raprcp.NavigationManagement
 
ListUtils - Class in bacnet.utils
 
ListUtils() - Constructor for class bacnet.utils.ListUtils
 
LNFCWT - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
 
load() - Method in class bacnet.datamodel.dataset.ExpressionData
Load information on the data: name, date, note, stat, etc ...
load() - Method in class bacnet.datamodel.dataset.ExpressionMatrix
Read compressed, serialized data with a FileInputStream.
load() - Method in class bacnet.datamodel.dataset.GeneExpression
 
load() - Method in class bacnet.datamodel.dataset.NGS
Load information on the datasets: name, date, note, stat, etc ...
load() - Method in class bacnet.datamodel.dataset.NTermData
Load NTermData from PATH_STREAMING+ this.getName() +EXTENSION
load() - Method in class bacnet.datamodel.dataset.ProteomicsData
Read compressed, serialized data with a FileInputStream.
load() - Method in class bacnet.datamodel.dataset.Tiling
 
load(boolean) - Method in class bacnet.datamodel.dataset.ExpressionData
Load information on the data: name, date, note, stat, etc ...
load(String) - Static method in class bacnet.datamodel.annotation.Annotation
Read compressed, serialized data with a FileInputStream.
load(String) - Static method in class bacnet.datamodel.annotation.Signature
Read compressed, serialized data with a FileInputStream.
load(String) - Method in class bacnet.datamodel.dataset.ExpressionData
Load information on the data: name, date, note, stat, etc ...
load(String) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
Read compressed, serialized data with a FileInputStream.
load(String) - Method in class bacnet.datamodel.dataset.Network
Load information of the data
load(String) - Static method in class bacnet.datamodel.dataset.NTermData
Load in: TranscriptomeData.PATH_STREAMING + nTermExpName + TranscriptomeData.EXTENSION Read compressed, serialized data with a FileInputStream.
load(String) - Static method in class bacnet.datamodel.expdesign.BioCondition
Read compressed, serialized data with a FileInputStream.
load(String) - Method in class bacnet.datamodel.expdesign.Experiment
Read compressed, serialized data with a FileInputStream.
load(String) - Static method in class bacnet.datamodel.proteomics.TIS
Read compressed, serialized data with a FileInputStream.
load(String) - Static method in class bacnet.datamodel.sequence.Gene
Load a serialized Gene
load(String) - Static method in class bacnet.datamodel.sequence.NcRNA
 
load(String) - Static method in class bacnet.datamodel.sequence.Operon
 
load(String) - Static method in class bacnet.datamodel.sequence.Sequence
Read compressed, serialized data with a FileInputStream.
load(String) - Static method in class bacnet.datamodel.sequence.Srna
 
load(String) - Static method in class bacnet.expressionAtlas.core.ComparisonAtlas
Read compressed, serialized data with a FileInputStream.
load(String) - Static method in class bacnet.genomeBrowser.core.Track
Load Track from a serialized file
load(String) - Static method in class bacnet.table.core.Filter
Prompt for a filename, and load a scribble from that file.
load(String) - Static method in class bacnet.utils.Filter
Prompt for a filename, and load a scribble from that file.
load(String, boolean) - Method in class bacnet.datamodel.dataset.ExpressionData
Load information on the data: name, date, note, stat, etc ...
load(String, Shell) - Static method in class bacnet.table.core.ColorMapper
 
load(String, Shell) - Static method in class bacnet.table.core.ColorMapperRCP
 
loadArrayHomologs(Sequence, String[][], ArrayList<String[]>, ArrayList<String[]>) - Static method in class bacnet.sequenceTools.GeneViewHomologTools
Load genome info and add homolog information on the column index1 and 2
loadCorrespondingChromosome(String) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
load and return the chromosome corresponding to an accession
loadEgdeGenome() - Static method in class bacnet.datamodel.sequence.Genome
Find in ModelProvider if Egde Genome is already loaded If not search EGDE_NAME in GENOMEDIR
loadEgdeGenome() - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
Find in ModelProvider if Egde Genome is already loaded If not search EGDE_NAME in GENOMEDIR
LoadExpressionMatrixHandler - Class in bacnet.handler
 
LoadExpressionMatrixHandler() - Constructor for class bacnet.handler.LoadExpressionMatrixHandler
 
loadFastaAddGeneFeaturesFromGeneIDGFF2(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm
loadFastaAddGeneFeaturesFromGeneMarkGTF(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
loadFastaAddGeneFeaturesFromGlimmerGFF3(File, File) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
loadFastaAddGeneFeaturesFromGmodGFF3(File, File, boolean) - Static method in class org.biojava3.genome.GeneFeatureHelper
Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application.
loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File, File, boolean) - Static method in class org.biojava3.genome.GeneFeatureHelper
 
loadFigureHomologs(Gene, Browser, ArrayList<String>) - Static method in class bacnet.sequenceTools.GeneViewHomologTools
Load SVG figure of phylogeny and replace all strain name by homolog informations
Save to JPG file and display it
loadFromText(String) - Static method in class bacnet.genomeBrowser.core.Track
Load a Track from a text file
loadGeneFromProteinId(String) - Static method in class bacnet.datamodel.sequence.Genome
Load proteinIdnToLocusTag hashmap for HomologCreation
loadGenome(String) - Static method in class bacnet.datamodel.sequence.Genome
Find in ModelProvider if Genome Accession is already loaded If not search load it
loadGenome(String) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
Find in ModelProvider if Genome Accession is already loaded If not search load it
loadGenome(String, boolean) - Static method in class bacnet.datamodel.sequence.Genome
Find in ModelProvider if Genome Accession is already loaded If not search load it If keepInMemory is true : Find in ModelProvider if Genome Accession is already loaded if not load it
If keepInMemory is false : Only load the Genome without saving it

loadGenome(String, String, boolean, boolean) - Static method in class bacnet.datamodel.sequence.Genome
Load/return a genome given by a genomeAccession ID

If keepInMemory is true : Find in ModelProvider if Genome Accession is already loaded if not load it
If keepInMemory is false : Only load the Genome without saving it

If annotation is true : Load annotation information of the genome
If anotation is false : Only load the sequence of the genome
loadGenome(String, String, boolean, boolean) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
Load/return a genome given by a genomeAccession ID

If keepInMemory is true : Find in ModelProvider if Genome Accession is already loaded if not load it
If keepInMemory is false : Only load the Genome without saving it

If annotation is true : Load annotation information of the genome
If anotation is false : Only load the sequence of the genome
loadHTML(String) - Method in class bacnet.views.InternalBrowser
 
loadLocalizationFigure(Browser, String[][], Sequence, String[][], Table, Genome) - Static method in class bacnet.sequenceTools.GeneViewLocalizationTools
Load SVG figure of phylogeny and replace all strain name by homolog informations
Save to JPG file and display it
loadMatrix() - Method in class bacnet.datamodel.dataset.GeneExpression
Load ExpressionMatrix found in TranscriptomeData.PATH_GENEXPR_NORM+getName()
loadMatrix() - Method in class bacnet.datamodel.dataset.Tiling
Load ExpressionMatrix found in TranscriptomeData.PATH_TILING_NORM + getName()
loadNetwork() - Method in class bacnet.views.CoExprNetworkView
Load the general Network
loadOldLocusTagFromLocusTag(String) - Static method in class bacnet.datamodel.sequence.Genome
Load locusTagToOldLocusTag hashmap for HomologCreation
loadOldLocusTagFromProteinId(String) - Static method in class bacnet.datamodel.sequence.Genome
Load proteinIDToOldLocusTag hashmap for HomologCreation
loadOperonsAndTerminator() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
Add Operons and Terminator from Annotation.EGDE_SUPPTABLE
This table comes directly from Wurtzel et al. annotation table
loadPhylogenomicFigure(ArrayList<String>) - Method in class bacnet.sequenceTools.GenomicsView
Load SVG figure of phylogeny and replace all strain name by homolog informations
Save to JPG file and display it
loadSignaturesNametoID(String) - Static method in class bacnet.datamodel.annotation.Signature
Load TreeMap<String,String> signaturesNametoID from text file in LIST_PATH
Used for initiating DATABASE.INSTANCE data provider
loadSrnas() - Method in class bacnet.datamodel.sequence.ChromosomeBacteriaSequence
Load all serialized Srna object found in Srna.PATHSerialize
loadTab(String, boolean) - Static method in class bacnet.datamodel.dataset.ExpressionMatrix
Load an ExpressionMatrix from a Tabdelimited text file
loadText(String) - Static method in class bacnet.datamodel.annotation.Signature
Read a formatted text file, and create the corresponding signature object
Each field of this text file, has to be separated by "#"
loadURL(String) - Method in class bacnet.views.InternalBrowser
 
loadXML(String) - Static method in class org.biojava3.core.util.XMLHelper
 
LOCAL - Enum constant in enum org.biojava3.core.sequence.DataSource
 
LOCALIZATION_LEGEND_PATH - Static variable in class bacnet.datamodel.annotation.SubCellCompartment
 
LOCALIZATION_PATH - Static variable in class bacnet.datamodel.annotation.SubCellCompartment
 
LocalizationDialog - Class in bacnet.sequenceTools
 
LocalizationDialog(Shell, String[][], Sequence, String[][], Genome) - Constructor for class bacnet.sequenceTools.LocalizationDialog
Create the dialog.
location() - Method in class org.biojava3.genome.parsers.gff.Feature
Get location of feature.
location() - Method in interface org.biojava3.genome.parsers.gff.FeatureI
Get the location of the feature.
location(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
location(int, int, Strand, int) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
location(List<Location>) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Used as a thin wrapper to the LocationHelper.location(java.util.List, java.lang.String) method to bring the given location list together as a join (the default type)
location(List<Location>, Integer, String) - Static method in class org.biojava3.core.sequence.location.template.Location.Tools
Used for building a location from a series of sub-locations
location(List<Location>, String) - Static method in class org.biojava3.core.sequence.location.LocationHelper
Builds a location from a List of locations; this can be circular or linear joins.
Location - Class in org.biojava3.genome.parsers.gff
A location on a sequence.
Location - Interface in org.biojava3.core.sequence.location.template
Sets of integers used to represent the location of features on sequence.
Location(int, int) - Constructor for class org.biojava3.genome.parsers.gff.Location
Construct new location from coordinates.
Location(Location) - Constructor for class org.biojava3.genome.parsers.gff.Location
Clone other location.
LOCATION_LENGTH - Static variable in class org.biojava3.core.sequence.features.AbstractFeature
Sort features by start position and then longest length.
Location.Tools - Class in org.biojava3.core.sequence.location.template
Helper methods for use with the Location classes.
LocationHelper - Class in org.biojava3.core.sequence.location
Helper methods for use with the Location classes.
LocationHelper() - Constructor for class org.biojava3.core.sequence.location.LocationHelper
 
LocIterator - Class in org.biojava3.genome.parsers.gff
Move a sliding window over a Location.
LocIterator(Location, int, int) - Constructor for class org.biojava3.genome.parsers.gff.LocIterator
Construct an iterator that slides a window over a Location.
LocusTag - Class in bacnet.datamodel.annotation
Since the update of RefSeq database all the locustag have been changed
Here is some methods to deal with this change
LocusTag() - Constructor for class bacnet.datamodel.annotation.LocusTag
 
LOCUSTAG_CHANGE_PATH - Static variable in class bacnet.scripts.listeriomics.PhylogenyListeriomics
 
log10(double[]) - Static method in class bacnet.utils.VectorUtils
log2(value)
log2(double) - Static method in class bacnet.utils.MathUtils
Calculate log with base 2
log2(double[]) - Static method in class bacnet.utils.VectorUtils
log2(value)
log2(double[][]) - Static method in class bacnet.utils.ArrayUtils
log2(value)
log2(ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
log2(values)
logFC(double[], double[]) - Static method in class bacnet.scripts.core.stat.StatUtils
 
LOGFC - Enum constant in enum bacnet.datamodel.dataset.OmicsData.ColNames
 
LOGFC - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
 
LOGFC - Enum constant in enum bacnet.table.core.ColorMapper.TypeMapper
 
LOGFC - Enum constant in enum bacnet.table.core.ColorMapperRCP.Type
 
longestCommonSub(String, String) - Static method in class bacnet.utils.ListUtils
The longest common subsequence (or LCS) of groups A and B is the longest group of elements from A and B that are common between the two groups and in the same order in each group.
For example, the sequences "1234" and "1224533324" have an LCS of "1234"
Code extract from http://rosettacode.org/wiki/Rosetta_Code
longestCommonSub(ArrayList<String>) - Static method in class bacnet.utils.ListUtils
From a list of String extract the longest common subsequence
LPE - Class in bacnet.scripts.core.stat
Class for calculating LPE statistics
Inspired from R library LPE
LPE - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
 
LPE() - Constructor for class bacnet.scripts.core.stat.LPE
 
LT - Class in bacnet.scripts.listeriomics.technology
 
LT() - Constructor for class bacnet.scripts.listeriomics.technology.LT
 
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