Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
P
- PADJ - Enum constant in enum bacnet.datamodel.dataset.OmicsData.ColNames
- paintComponent(Graphics) - Method in class bacnet.scripts.genome.CircularGenomeJPanel
- PAIRWISE - Enum constant in enum bacnet.scripts.blast.BlastOutput.BlastOutputTYPE
- parentGeneSequence - Variable in class org.biojava3.core.sequence.StartCodonSequence
- parentGeneSequence - Variable in class org.biojava3.core.sequence.StopCodonSequence
- parse(Reader) - Method in class org.biojava3.core.sequence.location.InsdcParser
-
Reader based version of the parse methods.
- parse(String) - Method in class org.biojava3.core.sequence.location.InsdcParser
-
Main method for parsing a location from a String instance
- parseColor(double) - Method in class bacnet.table.core.ColorMapper
- parseColor(double) - Method in class bacnet.table.core.ColorMapperRCP
- parseColorAWT(double) - Method in class bacnet.table.core.ColorMapperRCP
- parseData() - Static method in class bacnet.scripts.listeriomics.PhylogenyListeriomics
-
Using LOCUSTAG_CHANGE_PATH modify every table by changin locutag ID or removing the row if the gene is not found
- parseHeader(String, S) - Method in class bacnet.reader.NCBIFastaHeaderParser
-
Parse the header and set the values in the sequence
- parseHeader(String, S) - Method in class org.biojava3.core.sequence.io.GenericFastaHeaderParser
-
Parse the header and set the values in the sequence
- parseHeader(String, S) - Method in interface org.biojava3.core.sequence.io.template.FastaHeaderParserInterface
- parseInitURL(EPartService) - Static method in class bacnet.raprcp.NavigationManagement
-
Parse init URL and display the correct View with the correct view parameters
- parseName(String) - Static method in class bacnet.datamodel.expdesign.BioCondition
-
Parse a Comparison name, extracting leftBioCondition and rightBiocondition
- parseNewLocusTagChange() - Static method in class bacnet.datamodel.annotation.LocusTag
-
Create a HashMap with all "old_locus_tag" and "locus_tag" from the new GFF folder Listeriomics/NCBIGenomesNew/
- parseOldLocusTagChange() - Static method in class bacnet.datamodel.annotation.LocusTag
-
Create a HashMap with all "old_locus_tag" and "locus_tag" from the current GFF folder Listeriomics/NCBIGenomes/
- parsePhylogenomicFigure(String) - Static method in class bacnet.datamodel.phylogeny.Phylogenomic
-
Parse phylogenomic SVG figure and extract attributes corresponding to each genome
- ParserException - Exception in org.biojava3.core.exceptions
-
General abstraction of different parsing errors
- ParserException(Exception) - Constructor for exception org.biojava3.core.exceptions.ParserException
- ParserException(String) - Constructor for exception org.biojava3.core.exceptions.ParserException
- ParserException(String, Exception) - Constructor for exception org.biojava3.core.exceptions.ParserException
- parseStateParemeters(String) - Static method in class bacnet.raprcp.NavigationManagement
- parseWIGFile() - Static method in class bacnet.scripts.database.DNASeqCreation
-
Parse WIG file and calculate Copy Number Variation = raw coverage / mean coverage
The WIG has to be Raw number of reads per basepair - PATENTS - Enum constant in enum org.biojava3.core.sequence.DataSource
- PATH - Static variable in class bacnet.datamodel.sequence.Srna
-
Path for Srna raw data
- PATH - Static variable in class bacnet.expressionAtlas.core.ComparisonAtlas
- PATH - Static variable in class bacnet.expressionAtlas.core.GenomeElementAtlas
- PATH - Static variable in class bacnet.scripts.arrayexpress.ArrayExpressDataUtils
- PATH - Static variable in class bacnet.scripts.arrayexpress.ArrayExpressTechnology
- PATH - Static variable in class bacnet.scripts.genome.SDProfile
- PATH - Static variable in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressDataUtils
- PATH - Static variable in class bacnet.scripts.listeriomics.ArrayExpress.ArrayExpressTechnology
- PATH - Static variable in class bacnet.scripts.listeriomics.nterm.NTermStatProteolyse
- PATH - Static variable in class bacnet.scripts.listeriomics.nterm.RASToverlap
- PATH - Static variable in class bacnet.scripts.listeriomics.PhylogenyListeriomics
- PATH - Static variable in class bacnet.scripts.listeriomics.srna.SrnaTables
- PATH_ADD_IDENTITY - Static variable in class bacnet.scripts.database.HomologCreation
- PATH_ALLDataType - Static variable in class bacnet.scripts.core.Expression
- PATH_ALLExpMatrix - Static variable in class bacnet.scripts.core.Expression
- PATH_ALLGENEXPR - Static variable in class bacnet.scripts.core.Expression
- PATH_ALLRNASEQ - Static variable in class bacnet.scripts.core.Expression
- PATH_ALLTILING - Static variable in class bacnet.scripts.core.Expression
- PATH_ANNOTATION - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all supplementary information for genome annotation : Database.getInstance().getPath() + "/GenomeNCBI/Annotation/";
- PATH_BLAST - Static variable in class bacnet.scripts.database.HomologCreation
-
Path for Blast+
- PATH_BLAST_MAC - Static variable in class bacnet.scripts.blast.Blast
- PATH_BLAST_WIN - Static variable in class bacnet.scripts.blast.Blast
- PATH_BLASTDB - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for BlastDB folder
- PATH_BLASTDB - Static variable in class bacnet.scripts.database.HomologCreation
-
Path for BlastDB folder
- PATH_COMP - Static variable in class bacnet.expressionAtlas.core.ComparisonAtlas
- PATH_COMPARISONS - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for saving all comparisons datasets
- PATH_Conservation - Static variable in class bacnet.scripts.listeriomics.nterm.RASToverlap
- PATH_CONSERVATION - Static variable in class bacnet.datamodel.sequence.Srna
- PATH_Conservation_Cutoff - Static variable in class bacnet.scripts.listeriomics.nterm.RASToverlap
- PATH_CORRECTGENE - Static variable in class bacnet.datamodel.annotation.Annotation
-
Some EGD-e genes have same name, this file is used to correct gene name
- PATH_DATA - Static variable in class bacnet.scripts.core.UNAfold
- PATH_DATA - Static variable in class bacnet.utils.UNAfold
- PATH_DIFF_EXPR - Static variable in class bacnet.scripts.core.Comparison
- PATH_DIFF_LISTS - Static variable in class bacnet.scripts.core.Comparison
- PATH_EXPR_NORM - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all ExpressionMatrix RAW datasets
- PATH_EXPR_RAW - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all ExpressionMatrix RAW datasets
- PATH_GENEXPR_COMPLETE - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all GeneExpression COMPLETE datasets
- PATH_GENEXPR_NORM - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all GeneExpression NORM datasets
- PATH_GENEXPR_RAW - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all ExpressionMatrix NORM datasets
- PATH_GENOMES - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all Genomes : Database.getInstance().getPath() + "/GenomeNCBI/Genomes/";
- PATH_GENOMES_LIST - Static variable in class bacnet.scripts.blast.GenomeNCBIFolderTools
- PATH_GENOMES_LIST - Static variable in class bacnet.scripts.blast.MultiSequenceBlastProtein
- PATH_GENOMES_LIST - Static variable in class bacnet.scripts.blast.MultiSequenceTBlastNProtein
- PATH_GENOMES_NEW - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Deprecated.only used in Old Listeriomics database
- PATH_HOMOLOGS - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all homologs calculation file : Database.getInstance().getPath() + "/GenomeNCBI/Homologs/";
- PATH_INFOTABLE - Static variable in class bacnet.scripts.phylogeny.GenomePhylogeny
-
This table taken from Jolley et al.
- PATH_LIST - Static variable in class bacnet.scripts.listeriomics.nterm.NTermCreateFinalData
- PATH_MAC - Static variable in class bacnet.Database
-
Path when using MAC OX X
- PATH_NCBI_BacGenome - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBITools
- PATH_NGS_NORM - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all RNASeq NORM datasets
- PATH_NGS_RAW - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all RNASeq RAW datasets
- PATH_NORM - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all normalized datasets
- PATH_OLDLOCUSTAG - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all homologs calculation file : Database.getInstance().getPath() + "/GenomeNCBI/Homologs/";
- PATH_PROTEINID - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all homologs calculation file : Database.getInstance().getPath() + "/GenomeNCBI/Homologs/";
- PATH_PROTEINIDTOOLDLOCUSTAG - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all homologs calculation file : Database.getInstance().getPath() + "/GenomeNCBI/Homologs/";
- PATH_PROTEOMICS_NORM - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all Proteome NORM datasets
- PATH_PROTEOMICS_RAW - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all Proteome RAW datasets
- PATH_RAW - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all raw datasets
- PATH_RAW - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all raw data for Genomes : Database.getInstance().getPath() + "/GenomeNCBI/";
- PATH_RAW_DATA - Static variable in class bacnet.datamodel.proteomics.NTermCreateData
- PATH_RESULTS - Static variable in class bacnet.datamodel.proteomics.NTermCreateData
- PATH_RESULTS - Static variable in class bacnet.scripts.database.HomologCreation
-
Path for BlastDB folder
- PATH_SCRIPT - Static variable in class bacnet.scripts.database.HomologCreation
-
Path for data on the server when running homolog search blasts
- PATH_SEC_STRUCTURE - Static variable in class bacnet.datamodel.sequence.Srna
- PATH_STREAMING - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Path for all streaming datasets = serialized data for BACNET platform
- PATH_TermSeq_EGDe - Static variable in class bacnet.scripts.listeriomics.MainListeriomics
- PATH_TermSeq_EGDe - Static variable in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
- PATH_THREADS - Static variable in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Path for all homologs calculation file : Database.getInstance().getPath() + "/GenomeNCBI/Homologs/";
- PATH_THREADS - Static variable in class bacnet.scripts.database.HomologCreation
-
Path for BlastDB folder
- PATH_TILING_NORM - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all Tiling NORM datasets
- PATH_TILING_RAW - Static variable in class bacnet.datamodel.dataset.OmicsData
-
Folder for all Tiling RAW datasets
- PATH_TSS_EGDe - Static variable in class bacnet.scripts.listeriomics.MainListeriomics
- PATH_TSS_EGDe - Static variable in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
- PATH_TSS_Innocua - Static variable in class bacnet.scripts.listeriomics.MainListeriomics
- PATH_TSS_Innocua - Static variable in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
- PATH_TSSasRNA - Static variable in class bacnet.scripts.listeriomics.MainListeriomics
- PATH_TSSasRNA - Static variable in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
- PATH_WEBSITE - Static variable in class bacnet.Database
-
Path for website database on Pasteur Virtual Machine
- PATH_WIN - Static variable in class bacnet.Database
-
Path for website database on Windows
- PATH_WIN7 - Static variable in class bacnet.scripts.core.Rscript
- PATHFigure_ASrna - Static variable in class bacnet.datamodel.sequence.Srna
- PATHFigure_CISReg - Static variable in class bacnet.datamodel.sequence.Srna
- PATHFigure_Srna - Static variable in class bacnet.datamodel.sequence.Srna
- PATHSerialize - Static variable in class bacnet.datamodel.sequence.Srna
-
Path for serialized Srna before transferring data to Database
- PATHTABLE_ASrna - Static variable in class bacnet.datamodel.sequence.Srna
- PATHTABLE_CISReg - Static variable in class bacnet.datamodel.sequence.Srna
- PATHTABLE_Srna - Static variable in class bacnet.datamodel.sequence.Srna
- PATHTABLE_SrnaReference - Static variable in class bacnet.datamodel.sequence.Srna
- PATHXML - Static variable in class bacnet.datamodel.sequence.Srna
-
Path for Srna XML serialization for control
- PATHXML_10403S - Static variable in class bacnet.datamodel.sequence.Srna
-
Path for XML serialization for 10403S (Which have a specific annotation)
- PC - Enum constant in enum bacnet.datamodel.annotation.SubCellCompartment.TypeCompartment
- PDB1 - Enum constant in enum org.biojava3.core.sequence.DataSource
- PDB2 - Enum constant in enum org.biojava3.core.sequence.DataSource
- PDBe - Enum constant in enum org.biojava3.core.sequence.DataSource
- PDBWEB - Enum constant in enum org.biojava3.core.sequence.template.LightweightProfile.StringFormat
- pearsonCorrelation(double[], double[]) - Static method in class bacnet.utils.VectorUtils
- peptideLogo() - Static method in class bacnet.scripts.listeriomics.nterm.NTermStat
-
Create a fasta file with all sequences to create a logo
- Peptidomics - Class in bacnet.scripts.listeriomics
- Peptidomics() - Constructor for class bacnet.scripts.listeriomics.Peptidomics
- percentNucleotideSequence(String) - Static method in class org.biojava3.core.util.SequenceTools
- percentOverlap(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
Return percent overlap of two locations.
- performCancel() - Method in class bacnet.table.gui.ColorMapperWizard
- performCancel() - Method in class bacnet.table.gui.ColorMapperWizardPage
- performFinish() - Method in class bacnet.table.gui.ColorMapperWizard
- PERMUT - Enum constant in enum bacnet.scripts.core.stat.StatTest.TypeStat
- PFAM - Enum constant in enum org.biojava3.core.sequence.DataSource
- PHYLO_GENOME_SVG - Static variable in class bacnet.datamodel.phylogeny.Phylogenomic
- Phylogenomic - Class in bacnet.datamodel.phylogeny
- Phylogenomic() - Constructor for class bacnet.datamodel.phylogeny.Phylogenomic
- PhylogenomicsCreation - Class in bacnet.scripts.database
- PhylogenomicsCreation() - Constructor for class bacnet.scripts.database.PhylogenomicsCreation
- PhylogenyListeriomics - Class in bacnet.scripts.listeriomics
-
Different methods to create phylogeny tree, and tables for each genome elements
- PhylogenyListeriomics() - Constructor for class bacnet.scripts.listeriomics.PhylogenyListeriomics
- PhylogenySmallORFs - Class in bacnet.scripts.blast
-
Tools to blast a small ORF on other bacterial genomes, and display results on a phylogeny tree
- PhylogenySmallORFs - Class in bacnet.scripts.phylogeny
-
Tools to blast a small ORF on other bacterial genomes, and display results on a phylogeny tree
- PhylogenySmallORFs() - Constructor for class bacnet.scripts.blast.PhylogenySmallORFs
- PhylogenySmallORFs() - Constructor for class bacnet.scripts.phylogeny.PhylogenySmallORFs
- PhylogenyTools - Class in bacnet.scripts.phylogeny
-
Different methods to manipulate and display Newick and other phylogeny files
- PhylogenyTools() - Constructor for class bacnet.scripts.phylogeny.PhylogenyTools
- PhylogenyToolsJolley - Class in bacnet.scripts.phylogeny
-
This list of function is useful to manipulate Newick files given by Jolley in May 2012, from its publication Jolley et al.
- PhylogenyToolsJolley() - Constructor for class bacnet.scripts.phylogeny.PhylogenyToolsJolley
- PLASMID - Enum constant in enum org.biojava3.core.sequence.DNASequence.DNAType
- PLASTID - Enum constant in enum org.biojava3.core.sequence.DNASequence.DNAType
- plot2ann - Static variable in class bacnet.scripts.core.UNAfold
- plot2ann - Static variable in class bacnet.utils.UNAfold
- plot2Ann(String, String, String) - Static method in class bacnet.scripts.core.UNAfold
-
Convert a .ct file and .plot file into an .ann file
The output of plot2ann script is save into a .ann file - plot2Ann(String, String, String) - Static method in class bacnet.utils.UNAfold
-
Convert a .ct file and .plot file into an .ann file
The output of plot2ann script is save into a .ann file - plotFolding(String, int, String) - Static method in class bacnet.scripts.core.UNAfold
-
Run sir_graph software on a particular file
- plotFolding(String, int, String) - Static method in class bacnet.utils.UNAfold
-
Run sir_graph software on a particular file
- PLUGIN_ID - Static variable in class bacnet.scripts.Activator
- plus - Enum constant in enum bacnet.datamodel.proteomics.NTerm.MappingFrame
- plus() - Method in class org.biojava3.genome.parsers.gff.Location
-
Return location that is in same position on plus strand.
- plus(ExpressionMatrix, ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
-
Perform an addition between two ExpressionMatrix
First the intersection in term of RowNames and headers is found, then addition is done for each row - plusM - Enum constant in enum bacnet.datamodel.proteomics.NTerm.MappingFrame
- plusP - Enum constant in enum bacnet.datamodel.proteomics.NTerm.MappingFrame
- Point - Interface in org.biojava3.core.sequence.location.template
-
Holds a single point part of a location
- Point.Resolver<T extends Point> - Interface in org.biojava3.core.sequence.location.template
-
Used to resolve a position about a point
- populate(String) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Loops through the chars in a String and passes them onto
BitSequenceReader.BitArrayWorker.setCompoundAt(char, int) - populate(Sequence<C>) - Method in class org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker
-
Loops through the Compounds in a Sequence and passes them onto
BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int) - POSITIVE - Enum constant in enum org.biojava3.core.sequence.Strand
- possibleSmallRNAPeptides() - Static method in class bacnet.scripts.blast.ProteinTools
-
Get all possible peptides from EGD-e:
get all proteins sequence from Small RNAs get peptide sequence from M start to first R, or first E cut-off every peptide of size under 5aa export in a table usehttp://web.expasy.org/compute_pi/to calculate mass and isoelectric point save the different mass in NTermUtils.getPATH()+EGDePeptideMass.txt - possibleSmallRNAPeptides() - Static method in class bacnet.scripts.listeriomics.nterm.NTermDatabase
-
Get all possible peptides from EGD-e:
get all proteins sequence from Small RNAs get peptide sequence from M start to first R, or first E cut-off every peptide of size under 5aa export in a table usehttp://web.expasy.org/compute_pi/to calculate mass and isoelectric point save the different mass in NTermUtils.getPATH()+EGDePeptideMass.txt - pow2(double[]) - Static method in class bacnet.utils.VectorUtils
-
2^value
- pow2(double[][]) - Static method in class bacnet.utils.ArrayUtils
-
2^value
- pow2(ExpressionMatrix) - Static method in class bacnet.utils.ExpressionMatrixStat
-
2^values
- PredaTerm - Class in bacnet.scripts.core
-
PREDicting poly-A region and TERMinal splice acceptor for Leishmania Please read manuscript for details : Smith, M., Blanchette, M., Papadopoulou, B.
- PredaTerm() - Constructor for class bacnet.scripts.core.PredaTerm
- preDestroy() - Method in class bacnet.genomeBrowser.GenomeTranscriptomeView
- PREDICTED - Enum constant in enum org.biojava3.core.sequence.template.AbstractSequence.AnnotationType
- prefix(int) - Method in class org.biojava3.genome.parsers.gff.Location
-
The part of this location before the specified position.
- prefix(Location) - Method in class org.biojava3.genome.parsers.gff.Location
-
The part of this location before the other location (not inclusive).
- PRELOADED_ITEMS - Static variable in class bacnet.utils.RWTUtils
- PrettyXMLWriter - Class in org.biojava3.core.util
-
Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
- PrettyXMLWriter(PrintWriter) - Constructor for class org.biojava3.core.util.PrettyXMLWriter
- PRF - Enum constant in enum org.biojava3.core.sequence.DataSource
- PRIME - Static variable in class org.biojava3.core.util.Hashcoder
-
The prime number used to multiply any calculated hashcode seed by i.e. result = PRIME*result + c Where result is the result of the previous calculation (at first this will be seed) and c is the calculated int to add to result
- print(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
- print(String) - Method in interface org.biojava3.core.util.XMLWriter
-
Prints some textual content in an element.
- println(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
- println(String) - Method in interface org.biojava3.core.util.XMLWriter
-
Prints some textual content, terminated with a newline character.
- printRaw(String) - Method in class org.biojava3.core.util.PrettyXMLWriter
- printRaw(String) - Method in interface org.biojava3.core.util.XMLWriter
-
Send raw data to the stream.
- PROBES_PATH - Static variable in class bacnet.datamodel.dataset.GeneExpression
- PROBES_PATH - Static variable in class bacnet.datamodel.dataset.Tiling
- PROBES_PATH_2 - Static variable in class bacnet.datamodel.dataset.GeneExpression
- PROBES_PATH_2 - Static variable in class bacnet.datamodel.dataset.Tiling
- process() - Method in class org.biojava3.core.sequence.io.FastaGeneWriter
- process() - Method in class org.biojava3.core.sequence.io.FastaReader
-
The parsing is done in this method
- process() - Method in class org.biojava3.core.sequence.io.FastaWriter
- process(File, File, File, double, double, boolean, boolean) - Method in class org.biojava3.genome.query.OutputHitsGFF
- process(String) - Method in interface org.biojava3.core.sequence.io.util.IOUtils.ReaderProcessor
- process(String, String) - Method in class org.biojava3.genome.uniprot.UniprotToFasta
-
Convert a Uniprot sequence file to a fasta file.
- process(CompoundSet<?>) - Method in class bacnet.reader.FastaFileReader
-
The parsing is done in this method ******* There is a problem when the genes in the fasta file have the same Id, so I modify this method accordingly
- processAllData() - Static method in class bacnet.scripts.listeriomics.technology.UGiessen
-
Open every processed files and extract the different signal from it.
- processDanielRiboSeq() - Method in class bacnet.scripts.listeriomics.TSSNTermRiboSeqListeriomics
-
Process Daniel Dar TermSeq
- processGenomeName(String) - Static method in class bacnet.datamodel.sequenceNCBI.GenomeNCBI
-
Replace all spaces in genomeName by "_" to have folder name compatible for Blast search
All "_" already present are replaced by "--" - processNucleotides(File, String, File) - Method in class org.biojava3.genome.util.SplitFasta
- processReader(BufferedReader, IOUtils.ReaderProcessor) - Static method in class org.biojava3.core.sequence.io.util.IOUtils
-
Takes in a reader and a processor, reads every line from the given file and then invokes the processor.
- projectName - Static variable in class bacnet.e4.rap.BasicApplication
- projectName - Static variable in class bacnet.e4.rap.setup.BasicApplication
- proteinCreator(SequenceCreatorInterface<AminoAcidCompound>) - Method in class org.biojava3.core.sequence.transcription.TranscriptionEngine.Builder
- proteinfileExt - Static variable in class bacnet.reader.FastaFileReader
- ProteinSequence - Class in org.biojava3.core.sequence
-
The representation of a ProteinSequence
- ProteinSequence(String) - Constructor for class org.biojava3.core.sequence.ProteinSequence
-
Create a protein from a string
- ProteinSequence(String, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.ProteinSequence
-
Create a protein from a string with a user defined set of amino acids
- ProteinSequence(ProxySequenceReader<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.ProteinSequence
-
A protein sequence where the storage of the sequence is somewhere else.
- ProteinSequence(ProxySequenceReader<AminoAcidCompound>, CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.ProteinSequence
-
A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.
- ProteinSequenceCreator - Class in org.biojava3.core.sequence.io
-
Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.
- ProteinSequenceCreator(CompoundSet<AminoAcidCompound>) - Constructor for class org.biojava3.core.sequence.io.ProteinSequenceCreator
- ProteinTools - Class in bacnet.scripts.blast
- ProteinTools() - Constructor for class bacnet.scripts.blast.ProteinTools
- Proteome - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
- ProteomicsCreation - Class in bacnet.scripts.database
- ProteomicsCreation() - Constructor for class bacnet.scripts.database.ProteomicsCreation
- ProteomicsData - Class in bacnet.datamodel.dataset
-
OmicsData class inherited everything from ExpressionMatrix, the only difference is the TypeDate value, it a Proteome data.
It is not very useful for the moment but will be in the futur - ProteomicsData() - Constructor for class bacnet.datamodel.dataset.ProteomicsData
- ProteomicsDataFilterComposite - Class in bacnet.expressionAtlas
- ProteomicsDataFilterComposite(Composite, int, ProteomicsExpressionView) - Constructor for class bacnet.expressionAtlas.ProteomicsDataFilterComposite
- ProteomicsDataFilterComposite(Composite, int, ProteomicsView) - Constructor for class bacnet.expressionAtlas.ProteomicsDataFilterComposite
- ProteomicsExpressionView - Class in bacnet.expressionAtlas
- ProteomicsExpressionView() - Constructor for class bacnet.expressionAtlas.ProteomicsExpressionView
- ProteomicsView - Class in bacnet.expressionAtlas
- ProteomicsView() - Constructor for class bacnet.expressionAtlas.ProteomicsView
- ProxySequenceReader<C extends Compound> - Interface in org.biojava3.core.sequence.template
- pseudoGene - Enum constant in enum bacnet.datamodel.sequence.NcRNA.TypeNcRNA
- PTTReader - Class in bacnet.reader
- PTTReader() - Constructor for class bacnet.reader.PTTReader
- PURPLE - Static variable in class bacnet.utils.BasicColor
- pushState() - Method in class bacnet.e4.rap.InitViewBacnet
-
Push genome, chromosome, gene and Tabitem state
- pushState() - Method in class bacnet.e4.rap.InitViewListeria
-
Push genome, chromosome, gene and Tabitem state
- pushState() - Method in class bacnet.e4.rap.InitViewListeriaSample
-
Push genome, chromosome, gene and Tabitem state
- pushState() - Method in class bacnet.e4.rap.InitViewYersinia
-
Push genome, chromosome, gene and Tabitem state
- pushState() - Method in class bacnet.expressionAtlas.ProteomicsDataFilterComposite
- pushState() - Method in class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite
- pushState() - Method in class bacnet.genomeBrowser.NTerminomicsView
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Push genome, chromosome, gene and Tabitem state
- pushState() - Method in class bacnet.genomeBrowser.tracksGUI.TracksComposite
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Push states to change url
- pushState() - Method in class bacnet.sequenceTools.GeneView
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Push genome, chromosome, gene and Tabitem state
- pushState() - Method in class bacnet.sequenceTools.GenomicsView
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Push genome, chromosome, gene and Tabitem state
- pushState() - Method in class bacnet.sequenceTools.SrnaView
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Push genome, chromosome, gene and Tabitem state
- pushStateView(String) - Static method in class bacnet.raprcp.NavigationManagement
- pushStateView(String, HashMap<String, String>) - Static method in class bacnet.raprcp.NavigationManagement
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Push state puttin viewId and state parameters
stateName = viewID + key + "=" + parameters.get(key) + ";" - put(K, V) - Method in class org.biojava3.core.util.SoftHashMap
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Here we put the key, value pair into the HashMap using a SoftValue object.
- PVALUE - Enum constant in enum bacnet.datamodel.dataset.OmicsData.ColNames
- PyroGlu - Enum constant in enum bacnet.datamodel.proteomics.NTerm.TypeModif
- PYTHON_PATH - Variable in class bacnet.views.CRISPRPredictView
- PYTHON_PATH - Variable in class bacnet.views.CRISPRPredictView2
- PYTHON_SERVER - Variable in class bacnet.views.CRISPRPredictView
- PYTHON_SERVER - Variable in class bacnet.views.CRISPRPredictView2
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