U-Index

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U

UGiessen - Class in bacnet.scripts.listeriomics.technology
UGiessen() - Constructor for class bacnet.scripts.listeriomics.technology.UGiessen
UIBCLISTERIOMICS_PROJECT - Static variable in class bacnet.Database: Static variable to discriminate Listeriomics project from the others
unafold - Static variable in class bacnet.scripts.core.UNAfold
unafold - Static variable in class bacnet.utils.UNAfold
UNAfold - Class in bacnet.scripts.core
UNAfold - Class in bacnet.utils
UNAfold() - Constructor for class bacnet.scripts.core.UNAfold
UNAfold() - Constructor for class bacnet.utils.UNAfold
unafoldRNA(Sequence, String) - Static method in class bacnet.scripts.core.UNAfold: Run UNAFOld.pl Perl script
unafoldRNA(Sequence, String) - Static method in class bacnet.utils.UNAfold: Run UNAFOld.pl Perl script
uncompress(String, FileOutputStream) - Static method in class org.biojava3.core.util.UncompressInputStream
UncompressInputStream - Class in org.biojava3.core.util: This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).
UncompressInputStream(InputStream) - Constructor for class org.biojava3.core.util.UncompressInputStream
UNDEFINED - Enum constant in enum org.biojava3.core.sequence.Strand
union(String[], String[]) - Static method in class bacnet.utils.VectorUtils: Calculate union of two vector L1 and L2
union(ArrayList<String[]>) - Static method in class bacnet.utils.VectorUtils: Calculate the union of a list of Vector
union(ArrayList<String>, ArrayList<String>) - Static method in class bacnet.utils.ListUtils: Calculate union of two lists L1 and L2
union(ArrayList<ArrayList<String>>) - Static method in class bacnet.utils.ListUtils: Calculate the union of a list of lists
union(Location) - Method in class org.biojava3.genome.parsers.gff.Location: Return the union.
unionOFString(String, String) - Static method in class bacnet.utils.ListUtils: Complete a String, by adding elements from another String
CAREFULL: Both String should share a common sequence
unionOFString(ArrayList<String>) - Static method in class bacnet.utils.ListUtils: From a list of String extract the sequence regrouping all String
CAREFULL: All the String have to come from the same String.
UNIPROT - Enum constant in enum org.biojava3.core.sequence.DataSource
UniprotProxySequenceReader<C extends Compound> - Class in org.biojava3.core.sequence.loader: Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot.
UniprotProxySequenceReader(String, CompoundSet<C>) - Constructor for class org.biojava3.core.sequence.loader.UniprotProxySequenceReader: The uniprot id is used to retrieve the uniprot XML which is then parsed as a DOM object so we know everything about the protein.
UniprotToFasta - Class in org.biojava3.genome.uniprot
UniprotToFasta() - Constructor for class org.biojava3.genome.uniprot.UniprotToFasta
unknown - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
unknown - Enum constant in enum bacnet.datamodel.sequence.Sequence.SeqType
UNKNOWN - Enum constant in enum org.biojava3.core.sequence.DataSource
UNKNOWN - Enum constant in enum org.biojava3.core.sequence.DNASequence.DNAType
UNKNOWN - Enum constant in enum org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
unprocessGenomeName(String) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI: Go back to previous genomeName by eplacing all "_" by spaces
All "_" present before processing where replaced by "--" and are processed back
unZIP(String) - Static method in class bacnet.utils.FileUtils: Unziped a file in the same directory
unzipFile(String) - Static method in class bacnet.scripts.arrayexpress.ArrayExpressDataImport: Unzip processed files
update(byte[], int, int) - Method in class org.biojava3.core.util.CRC64Checksum
update(int) - Method in class org.biojava3.core.util.CRC64Checksum
update(String) - Method in class org.biojava3.core.util.CRC64Checksum
updateAllElements(Genome) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeConversion: Add all elements found in the Chromosome to LinkedHashMap<String, Sequence> allElements
updateAllGeneOmicsInfo() - Method in class bacnet.sequenceTools.GeneView: Update all the information for the gene selected:
Homolog update Load localization Update synteny view Transcriptome update Proteome update
updateAllWidgets() - Method in class bacnet.sequenceTools.SrnaView: Update all panels and info after a gene selection
updateBioConditionList() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
updateBioConditionList() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
updateBioConditionTable() - Method in class bacnet.expressionAtlas.ProteomicsExpressionView: Update Table for Biological Condition
updateBioConditionTable() - Method in class bacnet.expressionAtlas.ProteomicsView: Update Table for Biological Condition
updateBioConditionTable() - Method in class bacnet.expressionAtlas.TranscriptomicsView: Update Table for Biological Condition
updateColorCanvas(GC, int, int, ColorMapper) - Static method in class bacnet.table.gui.ColorMapperWizardPage
updateDisplayedElements() - Method in class bacnet.expressionAtlas.HeatMapMultiOmicsView: Update the list of rows to exclude from the display
updateExclude() - Method in class bacnet.table.core.FilterList
updateExcludeColumns(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapProteomicsExpressionView: Update the list of columns from the display
updateExcludeColumns(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapProteomicsView: Update the list of columns from the display
updateExcludeColumns(ArrayList<String>) - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView: Update the list of columns from the display
updateExcludeRows() - Method in class bacnet.expressionAtlas.HeatMapProteomicsView: Update the list of rows to exclude from the display
updateExcludeRows() - Method in class bacnet.expressionAtlas.HeatMapTranscriptomicsView: Update the list of rows to exclude from the display
updateExpressionAtlas() - Method in class bacnet.sequenceTools.SrnaView: Update display of expression data results
updateExpressionAtlas(Sequence, Text, GeneView, String[][]) - Static method in class bacnet.sequenceTools.GeneViewTranscriptomeTools: Update display of expression data results
updateGeneBasicInfo() - Method in class bacnet.sequenceTools.GeneView
updateGeneInfo() - Method in class bacnet.sequenceTools.GeneView: Update all the information for the gene selected:
Homolog update Load localization Update synteny view Transcriptome update Proteome update
updateGeneOmicsInfo() - Method in class bacnet.sequenceTools.GeneView: Update all the information for the gene selected:
Transcriptome update Proteome update
updateGenome() - Method in class bacnet.sequenceTools.SrnaView
updateGenomeViewer() - Method in class bacnet.sequenceTools.GeneView: Update genome viewer
updateHomolog() - Method in class bacnet.sequenceTools.GeneView
updateHomologTable(TableViewer, String[][], ArrayList<String[]>, ArrayList<String[]>, BioConditionComparator, ArrayList<String>, ArrayList<String>, Text) - Static method in class bacnet.sequenceTools.GeneViewHomologTools: Update Table for Biological Condition
updateInfo() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite: From finalarrayBioCondition update the text for every Checkbox
updateInfo() - Method in class bacnet.expressionAtlas.TableCompositeHeatMap: Update all viewers and labels
updateInfo() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite: From finalarrayBioCondition update the text for every Checkbox
updateInfo() - Method in class bacnet.table.TableSWTComposite: Update all viewers and labels
updateInfoFromChromosome(LinkedHashMap<String, ChromosomeBacteriaSequence>) - Static method in class bacnet.reader.FastaFileReader: According to the info we found in Chromosomes, we update the info of the different components (coding, ncoding, proteins)
updateProteinAtlas(Sequence, Text, GeneView, String[][]) - Static method in class bacnet.sequenceTools.GeneViewProteomeTools: Update display of expression data results
updateProteomesTable(Sequence, GeneView, String[][]) - Static method in class bacnet.sequenceTools.GeneViewProteomeTools: Update proteomics table = Protein expression with a value over 0
updateTable() - Method in class bacnet.sequenceTools.SrnaView
updateTranscriptomesTable(Sequence, GeneView, String[][]) - Static method in class bacnet.sequenceTools.GeneViewTranscriptomeTools: Update transcriptomes table = transcript expression with a value over 0
updateView() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
updateView() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
updateView() - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
updateView() - Method in class bacnet.sequenceTools.SequenceDisplayDialog
updateView(IProgressMonitor) - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
upstream(int) - Method in class org.biojava3.genome.parsers.gff.Location: Return the adjacent location of specified length directly upstream of this location.
URY_YERSINIOMICS_PROJECT - Static variable in class bacnet.Database: Static variable to discriminate Listeriomics project from the others
userData() - Method in class org.biojava3.genome.parsers.gff.Feature: Get HashMap of user data.
userData() - Method in interface org.biojava3.genome.parsers.gff.FeatureI: Get HashMap of user data.

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