All Classes and Interfaces
Class
Description
The details of a Compound
A feature is currently any descriptive item that can be associated with a sequence position(s) A
feature has a type and a source which is currently a string to allow flexibility for the user
Ideally well defined features should have a class to describe attributes of that feature
Base abstraction of a location which encodes for the majority of important features about a
location such as the start, end and strand
The base class for DNA, RNA and Protein sequences.
A location which is bound to an AccessionID.
Indicates an entity is accessioned
Used in Sequences as the unique indentifier.
OSGI Activator of bacnet.e4.rap.setup
OSGI Activator of bacnet.scripts
Used to describe an Amino Acid.
Set of proteinogenic amino acids.
Hello world!
All the methods which are specific to a webpage
Different methods to curate and parse the different data for Listeriomics website
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE
List of methods to download all ArrayExpress needed for Listeriomics website
Different methods to curate and parse the different data for Listeriomics website
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE
Different methods to curate and parse the different data for Listeriomics website
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE
ONLY METHODS BEFORE FINAL DATA PROCESSING ARE PRESENT HERE
List of methods to determine the different technology used
List of methods to determine the different technology used
Stores a Sequence as a collection of compounds in an ArrayList
Public class with general array manipulation utilities, not specific to PROJECTNAME.
Bare bones version of the Sequence object to be used sparingly.
This class is used for the different bioconds declared in the experiment
It contains the biocond name, and all the related data.
An implementation of the popular bit encodings.
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.
Different methods to create blast database for the genome, the ORF, and the smallORF
This comparator classify the BlastResult by their position on the genome
Need to keep track of actual bytes read and take advantage of buffered reader performance.
Attempts to wrap compounds so it is possible to view them in a case insensitive manner
A sequence creator which preserves the case of its input string in the user collection of the
returned ProteinSequence.
Represents a exon or coding sequence in a gene.
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
A ChromosomeSequence is a DNASequence but keeps track of geneSequences
Circular Genome Panel created for displaying Small RNAs in CGView
This object represents a classpath resource on the local system.
Class for managing triplet of nucleotides.
Allo<s detection of start and stop codons in nucleotide sequences
Allo<s detection of start and stop codons in nucleotide sequences
Define a codon
Tools for calculating codon Usage of amino acid sequences
Codon Usage tables came from : http://www.kazusa.or.jp/codon/
Codon Usage tables came from : http://www.kazusa.or.jp/codon/
Class for finding every combination of a set of integer
A ComparisonAtlas is related to a Comparison object and gives the list of genome elements over,
under and not differentially expressed
For a given sequence this class will create a view over the top of it and for every request the
code will return the complement of the underlying base e.g. base A will become base T
NTerm composite which is displayed on the right of the GenomeViewer.
Static utility to easily share a thread pool for concurrent/parallel/lazy execution.
Utility class that calculates a CRC64 checksum on a stream of bytes.
A ModelProvider specifically design for the Website Database
Contains persistent variable, used through all the website.
Contains persistent variable, used through all the website.
Class for loading databases in a thread
Deprecated.
If a SequenceProxyReader implements this interface then that external source has a list of cross
reference id(s)
GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ,
DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research
Foundation prf||name SWISS-PROT UNIPROT sp|accession|name Brookhaven Protein Data Bank (1)
pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents
pat|country|number GenInfo Backbone Id bbs|number General database identifier
gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier
lcl|identifier
If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein
is known by.
This is class should model the attributes associated with a DNA sequence
The type of DNA sequence
A helper class that allows different ways to read a string and create a DNA sequence.
Performs the first stage of transcription by going from DNA to RNA.
Specific tools for downloading files from eclipse.rap instance NEED TO BE COMMENTED FOR
Eclipse.RCP to work !!!
Interface for carrying out edit operations on a Sequence.
Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an
editing Sequence should be joined together with a target Sequence.
Implementation which allows for the deletion of bases from a Sequence
Edit implementation which allows us to insert a base at any position in a Sequence.
Allows for the substitution of bases into an existing Sequence.
List of method for creating EGDe_Mean data: A data created from the mean of all Wild Type data
(37C in BHI)
A set of helper methods which return true if the two parameters are equal to each other.
Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a
negative stranded gene should go the other direction.
A gene contains a collection of Exon sequences
A list of methods to combine transcriptomics data in ExpressionMatrix
Abstract Class describing data related to transcriptome
This data are saved in DataStream and might be read in streaming mode
boolean[] read is used as a "read" indicator
As soon as a position in double[] values has been read, boolean[] read is updated
This data are saved in DataStream and might be read in streaming mode
boolean[] read is used as a "read" indicator
As soon as a position in double[] values has been read, boolean[] read is updated
This is the principal data model used in the software for managing big table of expression
List of method for doing Stat on ExpressionMatrices
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to
3 prime version.
Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be
the primary class used to read Fasta files
Used to parse a stream of a fasta file to get the sequence
The FastaWriter writes a collection of sequences to an outputStream.
The class that should be used to write out fasta file of a sequence collection
A Feature corresponds to a single row in a GFF file.
A feature on a sequence (for example, an exon or a gene), defined by a location and a set of
attributes encoded as key/value pairs.
Interface class to handle describing arbitrary features.
A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
Models the keywords that are annotated for a protein sequence at Uniprot.
Thrown from SequenceFileProxyLoader if error opening file using RandomnAccessFile
This class is a good example of using the SequenceCreatorInterface where during parsing of the
stream the sequence and the offset index are passed to create a Protein sequence that will be
loaded in lazily.
This class is a good example of using the SequenceCreatorInterface where during parsing of the
stream the sequence and the offset index are passed to create a Protein sequence that will be
loaded in lazily.
Utils for file manipulation.
Dialog for managing
Filter for ExpressionMatrixDialog displaying the list of
Filters currently used on the
ExpressionMatrixProvides a cache for storing multiple small files in memory.
Four bit encoding of the bit formats.
A four bit per compound implementation of the bit array worker code.
Indicates a way of translating a sequence.
Implementation for resolving fuzzy locations.
GenBankl reader tools
TO BE FIXED for adding other chromosomes
TO BE FIXED for adding other chromosomes
Here are all the methods for displaying each Genome element
GeneExpression array data from Listeria tiling chip ArrayExpress id : A-AFFY-140
Here double[] values vector has length = 5*probes.size because we put 5 columns column 0-2 = 3
replicatas column 3 = median expression column 4 = var expression
Allow to process genome elements annotation
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
List of tools useful to extract information hidden in the NoteList of a DNASequence
We store the original header if the sequence is parsed from a fasta file and will use that exact
sequence if we write out the sequences to a fasta file.
The default fasta header parser where some headers are well defined based on the source database
which allows us to set the source of the protein sequence and the identifier that can be used in
future implementations to load features from external sources
If the user has a custom header with local data then they can create their own implementation of
a FastaHeaderParserInterface
GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ,
DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research
Foundation prf||name SWISS-PROT sp|accession|name Brookhaven Protein Data Bank (1)
pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE PDB EBI
PDB:1ECY_A mol:protein length:142 ECOTIN Patents pat|country|number GenInfo Backbone Id
bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence
ref|accession|locus Local Sequence identifier lcl|identifier
All the tools to display homologs in the Gene Panel view: - It creates the homolog table - Create
the homolog figure - Display both of them
Class for managing Genome
Contains all Genes, non-coding RNA and all other elements found in the genome GFF
Contains all Genes, non-coding RNA and all other elements found in the genome GFF
GFFNCBIReaderStatic methods for converting GenomeNCBI to Genome
Genome is used for fast loading of all genomic information we gathered
Genome is used for fast loading of all genomic information we gathered
Object containing an entire genome, created from NCBI RefSeq data
Data for this genome come from: NCBI.fna (for the sequence) NCBI.gff (for Gene, CDS,
and ncRNA lists) If it exists some information are added: Rfam.gff (other info) supp
info in a .txt file supp info about RAST results in a .txt file For EGD-e only:
Srna.xml are read to add to the genome
Data for this genome come from:
Manage phylogeny from MLST scheme : Jolley and others
List of tools available for genome creation
Display on the genome viewer: expression of specific bioCond and the log of fold change
http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
Read GFF files to create a
Genome objectContains helper methods for generating a HashCode without having to resort to the commons lang
hashcode builders.
Currently not used
List of methods to manage D3js visualization in BACNET
Methods link to image mlanipulation with ImageMagick
A class that provides an InputStream from a File.
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.
Used to represent bond locations equivalent to bond(7,8) or bond(7).
Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3'
ordering is defined.
Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g.
Used to describe a 5' to 3' ordering but no firm assurance it is correct
Parser for working with INSDC style locations.
Closure interface used when working with
IOUtils#processReader(String).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.
Holds the concept of a codon table from the IUPAC format
This reader actually proxies onto multiple types of sequence in order to allow a number of
sequence objects to act as if they are one sequence.
Defines a minimal data structure for reading and writing a sequence alignment.
List of output formats.
Sets of integers used to represent the location of features on sequence.
A location on a sequence.
Helper methods for use with the Location classes.
Helper methods for use with the Location classes.
Move a sliding window over a Location.
Since the update of RefSeq database all the locustag have been changed
Here is some methods to deal with this change
Here is some methods to deal with this change
Class for calculating LPE statistics
Inspired from R library LPE
Inspired from R library LPE
Implements a minimal data structure for reading and writing a sequence alignment.
Every lmethods for managing navigation state in eclipse.rap application.
My own implementation of a FastaHeaderParserInterface to parse Fasta files from NCBI ftp
NCBI fna (genome and plasmids) gi|gi-number|ref|accession|name gi|16802048|ref|NC_003210.1|
Listeria monocytogenes EGD-e, complete genome NCBI ffn (coding) ref|refGenome
gi-number|:start-end name ref|NC_003210.1|:318-1673 chromosomal replication initiation protein
[Listeria monocytogenes EGD-e] NCBI frn (non-coding) ref|refGenome gi-number|:start-end| name|
[locus-tag] ref|NC_003210|:82705-82777|Lys tRNA| [locus_tag=lmot01] NCBI faa (proteins)
gi|gi-number|ref|accession|name gi|16802049|ref|NP_463534.1| chromosomal replication initiation
protein [Listeria monocytogenes EGD-e]
Network object for co-expression network analysis and visualisation
Class for manipulating various RNASeq data, herited from ExpressionData
double[] value is of genome size, when ones want to see RNAseq expression at a certain bp position, just extract values[bpposition]
Need to be loaded first, and unlog has RNASeq will be logged for display when convert in the platform
double[] value is of genome size, when ones want to see RNAseq expression at a certain bp position, just extract values[bpposition]
Need to be loaded first, and unlog has RNASeq will be logged for display when convert in the platform
Object for managing every mapped sequences
Type of modification at the start of a peptide
Run different method to compare iTIS position (internal translation) to data of Ribosome
profiling in Bacillus and Ecoli:
compare the gene by BlastN find internal translation in the ribosome profiling find internal SD sequence
compare the gene by BlastN find internal translation in the ribosome profiling find internal SD sequence
Transform excel table describing all N-Terminal peptides found in Listeria
Find the position of each peptide in Listeria genome create a NGS data from it
Find the position of each peptide in Listeria genome create a NGS data from it
Genertal class for creation of NTerminomics tables
General method for running all methods related to NTerm project
List of method to do statistics about common features in N-Terminus of genes: - start codon - SD
binding - AU proportion - Folding energy
A list of methods to assess the quantity of proteolysis on the peptides
List of methods for creating Summary Table for TIS
Using NTermFilter we have regroup TIS in different overlap groups, which we use now to create the Summary Tables.
Using NTermFilter we have regroup TIS in different overlap groups, which we use now to create the Summary Tables.
Abstract Class describing data related to omics data
Enum referencing the different type of OmicsData possible:
GeneExpr
Tiling
RNASeq
TSS (Transcription Initiation Site)
NTerm (Translation Initiation Site)
Proteome (Matrix of protein found)
MassSpec (List of peptides found by mass spectrometry)
ExpressionMatrix (General matrix format)
unknown
Run thread for opening BioCondition, Comparisons, detect Genome and open corresponding LogFC
ExpressionMatrix
General abstraction of different parsing errors
Different methods to create phylogeny tree, and tables for each genome elements
Tools to blast a small ORF on other bacterial genomes, and display results on a phylogeny tree
Tools to blast a small ORF on other bacterial genomes, and display results on a phylogeny tree
Different methods to manipulate and display Newick and other phylogeny files
This list of function is useful to manipulate Newick files given by Jolley in May 2012, from its
publication Jolley et al.
Holds a single point part of a location
Used to resolve a position about a point
PREDicting poly-A region and TERMinal splice acceptor for Leishmania Please read manuscript for
details : Smith, M., Blanchette, M., Papadopoulou, B.
Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
The representation of a ProteinSequence
Used to create a ProteinSequence from a String to allow for details about the location of the
sequence etc.
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
It is not very useful for the moment but will be in the futur
DNA Sequences produced by modern sequencers usually have quality informaion attached to them.
It is common to have a numerical value or values associated with a feature.
List of methods for adding RAST genes to EGD-e annotation
Methods to look at overlapping elements between NCBI and RAST genomes
Utility class for managing OS resources associated with SWT/JFace controls such as colors, fonts,
images, etc.
!!!
Provider for plugin resources, used by WindowBuilder at design time.
For a given sequence this class will return the base at the reversed position i.e. in a sequence
of size 10, if you request base 2 you will get back the base at position 9.
RNASequence where RNACompoundSet are the allowed values
Used to create a RNA sequence
Attempts to do on the fly translation of RNA by not requesting the compounds until asked.
Takes a
Sequence of NucleotideCompound which should represent an RNA sequence
(RNASequence is good for this) and returns a list of Sequence which hold
AminoAcidCompound.Tools for saving files
Everything in bacnet.raprcp package is specific to eclipse.rap or eclipse.rcp.
Everything in bacnet.raprcp package is specific to eclipse.rap or eclipse.rcp.
Utils methods for managinf files.
Calculate Shine-Dalgarno profile for bacterial genome.
Dialog which allow specific selection of genes, smallRNAs and cisRegs
Object for manipulating part of Sequence.
Main attributes are
SeqType {Gene,NcRNA,Operon,Srna,ASrna,terminator,unknown}
for each
Main attributes are
name, begin, end, strand, genome, and typeSeqType {Gene,NcRNA,Operon,Srna,ASrna,terminator,unknown}
for each
Sequence we force the condition: this.begin inf_to this.endMain interface for defining a collection of Compounds and accessing them using biological indexes
This is a common method that can be used across multiple storage/proxy implementations to handle
Negative strand and other interesting elements of sequence data.
Used to sort sequences
This class represents the storage container of a sequence stored in a fasta file where the
initial parsing of the file we store the offset and length of the sequence.
Currently not used
A location in a sequence that keeps a reference to its parent sequence
Provides a set of static methods to be used as static imports when needed across multiple
Sequence implementations but inheritance gets in the way.
A basic sequence iterator which iterates over the given Sequence by biological index.
A static class that provides optimization hints for memory or performance handling of sequence
data.
General methods for session control of an eclipse.rap application
SetupPart for initialisation and creation of the Database
Very basic implementation of the Location interface which defines a series of simple
constructors.
Basic implementation of the Point interface.
An implementation of the SequenceReader interface which for every call will return only 1
compound (given to it during construction; a String is also valid but will require a
CompoundSet).
Deprecated.
A in memory cache using soft references.
Utility to write each Fasta entry to a unique file
List of methods to manage Srna data for Listeriomics
Include a list of Methods to read every Table containing Small RNAs in Listeria
For each it reads the
For each it reads the
Table and create a List of SrnaCalculate presence of start codon on firrst chromosome of bacterial genomes
Used to map the start codon feature on a gene
Used to map the stop codon sequence on a gene
Provides a way of representing the strand of a sequence, location hit or feature.
A utility class for common
String manipulation tasks.An example of a ProxySequenceReader that is created from a String.
All data and methods for Subcellular compartment information are done here
Methods for creating the different figures and Tables of the paper
Utility class for managing OS resources associated with SWT controls such as colors, fonts,
images, etc.
List of method to create Co-expression network and analyse it
Provides a way of separating us from the specific
IUPACParser.IUPACTable even though this is the only
implementing class for the interface.Class used to hold three nucleotides together and allow for equality to be assessed in a case
insensitive manner.
Instance of a Codon which is 3
NucleotideCompounds, its corresponding
AminoAcidCompound and if it is a start or stop codon.The Composite in which is displayed the heatmap
A sequence can be associated with a species or Taxonomy ID
All methods which will be executed before or after interface run
A implmentation of AbstractFeature
Tiling array data from Listeria tiling chip ArrayExpress id : A-MEXP-1572 *
This class is used to regroup different Nterm.
A TrackCanvasData is the Canvas in which will be displayed datasets
A TrackCanvasGenome is the Canvas in which will be displayed genome annotation
In TracksComposite both
TrackCanvasData and TrackCanvasGenome will be
displayed.Used as a way of encapsulating the data structures required to parse DNA to a Protein sequence.
This class is the way to create a
TranslationEngine.List of methods to add the different transcriptomic datasetsto your multi-omics website
View in which is displayed the table with all transcriptomics data available
This is the sequence if you want to go from a gene sequence to a protein sequence.
Thrown from AbstractCompundTranslator
List of methods to process TSS, TermSeq, and RiboSeq of Listeriomics Some TSS and NTerm lists
were provided in tab-delimited format.
Implementation of the 2bit encoding.
Extension of the BitArrayWorker which provides the 2bit implementation code.
This class decompresses an input stream containing data compressed with the unix "compress"
utility (LZC, a LZW variant).
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.
Variance normalization methods which will reduce the total variance of each data to 1
For each column of the ExpressionMatrix, multiply each value by: Math.sqr(1/var(x))
So final variance of each column is equal to zero
For each column of the ExpressionMatrix, multiply each value by: Math.sqr(1/var(x))
So final variance of each column is equal to zero
Vector are array with one dimension like :
String[] or double[]Class for creating sets necessary in Venn diagrams
Providing a list of sets (through
Providing a list of sets (through
ArrayList) it will find intersections,
unions and differences between all sets.A sliding window view of a sequence which does not implement any interfaces like
Sequence
because they do not fit how this works.Simple interface for building XML documents.