All Classes and Interfaces
Class
Description
Encapsulates the ActSiteFeature of a
UniProtEntry.Details a blast alignment.
Maximum number of match alignments reported in the result output.
Adds an extra field to the
GoAnnotation interface.The RA (Reference Author) lines list the authors of the paper (or other work)
cited.
Used in the flatfile either in the RA or the RG line The RG line The
Reference Group (RG) line lists the consortium name associated with a given
citation.
Input parameters to configure a blast request.
Container that wraps a blast result.
Base blast service interface.
Holds a blast result for a given entry.
The BLAST program to be used for the blast.
A variation of the RL line format is used for papers found in books or other
types of publication, which are then cited using the following format:
RL (In) Editor_1 I.[, Editor_2 I., Editor_X I.] (eds.); RL Book_name,
pp.[Volume:]First_page-Last_page, Publisher, City (YYYY).
A book can in the SwissProt flatfile fromat have besides a title have a name
This might be a sub title or other memnomic for a book.
Encapsulates the CarbohydFeature of a
UniProtEntry.Encapsulates the ChainFeature of a
UniProtEntry.The basic type containing the common values that are present in each and
every Citation
Created by IntelliJ IDEA.
User: Emilio Salazar Date: 27-Oct-2005
Created by IntelliJ IDEA.
Created by IntelliJ IDEA.
Client class is the starting point for JAPI client.
Specification for configuring a client and used by the
Client.Description of A cofactor: any non-protein substance required for an enzyme
to be catalytically active
A Comment in the
Notes: public void setCommentType(CommentType type);
removed because it causes havoc if textual comments change into structured ones.
UniProtEntry.Notes: public void setCommentType(CommentType type);
removed because it causes havoc if textual comments change into structured ones.
CommentFreeText is used by TextOnlyComment to support multitext comments
Created by IntelliJ IDEA.
Evidence on how the comment was derived.
Free text comment, has EvidencedValue and hasCommentStatus used in free text
comment
Enumerates all comment types in UniProt.
COMPBIAS - Extent of a compositionally biased region.
User: mkleen@ebi.ac.uk Date: 18-Nov-2005 Time: 14:17:39
Created by IntelliJ IDEA.
Created by IntelliJ IDEA.
The DBCrossReference annotation of the
UniProtEntry.The set UniProt of databases one can blast against.
Created by IntelliJ IDEA.
A list of all Cross reference databases in UniProt.
Cross Reference database definitions
Here is the example of the definition for EMBL and IntAct
Container used to represent the definition of the disease.
A name by which the disease is also known as.
Description of the disease(s) associated with a deficiency of a protein
Generic description of the disease.
Identifier of the disease within the disease controlled vocabulary file
humdisease.txt.
Contains text describing the manifestation of a particular disease on a
particular protein.
Reference of an external source the best describes the disease
The identifier of the disease provided by the external source
DiseaseReferenceTypeEnumeration of the possible external sources that have a references to
diseases.
DOMAIN - Extent of a domain, which is defined as a specific combination of
secondary structures organized into a characteristic three-dimensional
structure or fold.
The amount a score can drop before gapped extension of word hits is halted.
The RL line for an electronic publication includes an '(er)' prefix.
An EntryAudit of a
UniProtEntry.Implemented by all entries describing a protein sequence.
The Evidence annotation of the
UniProtEntry.The EvidenceAttribute of the
Evidence.The EvidenceCategory of the
Evidence.The EvidenceCode of the
Evidence.Most of data in uniprot has evidence EvidencedValue is for this type of data
This interface extends Value and HasEvidences
The EvidenceId of the
Evidence.The EvidenceOriginName of the
Evidence.The EvidenceType of the
Evidence.Defines which status can be assigned to a Swissprot Feature.
Stores the sub category type of a specific category as well as the respective
value.
Defines the set of valid field types
Current valid fields are: Full, Short, EC, Allergen, Biotech, CD_antigen,
INN.
Filter regions of low sequence complexity.
Contains a flag descriptors found within a DE line
along with any evidences
Contains a list of acceptable flag descriptors found within a DE line
current valid flags are Precursor, Fragment, Fragments
About This Data Structure
Created by IntelliJ IDEA.
About This Data Structure
About This Data Structure
Represents a GO ECO evidence
This code is autogenerated by the class uk.ac.ebi.util.autocode.AutoCoder.
Models the relationship between a UniProt protein and all the GO terms
associated to it
Indicates that a
Feature in an
UniProtEntry can have an alternative sequence
(SubSequence).Created by IntelliJ IDEA.
Created by IntelliJ IDEA.
This interface is used for all types that have a Date attached.
The superclass of all annotation items in a
UniProtEntry, which can be tagged with evidence tags.Indicates that a
Feature in an
UniProtEntry can have a
FeatureId.HasFreeText interface is for all Free text notes.
Container for the blast result of a given entry
User: mkleen@ebi.ac.uk Date: 28-Nov-2005 Time: 11:24:21
The RL line for a journal citation includes the journal abbreviation, the
volume number, the page range and the year.
A single Keyword in the Keyword annotation of the
UniProtEntry.Created by mkleen@ebi.ac.uk Date: 14-Sep-2007 Time: 15:02:43
Enumeration for all possible selections for similarity matrizes used for the BLAST service.
Created by IntelliJ IDEA.
MOD_RES - Posttranslational modification of a residue.
MUTAGEN - Site which has been experimentally altered.
Maps the Names of a protein in a DE line : RecName, AltName, SubName
As an example:
As an example:
Conatins a list of acceptable values for the categories expressed in a DE
line
Encapsulates a single taxon in the taxonomy annotation of the
UniProtEntry.Defines a Taxon as represented in the NEWT database.
NON_TER - The residue at an extremity of the sequence is not the terminal
residue.
About This Data Structure
About This Data Structure
Encapsulates a single gene coding of the
UniProtEntry.About This Data Structure
About This Data Structure
Interface to an Organism Host used in an UniProtKB entry.
About This Data Structure
About This Data Structure
About This Data Structure
Created by IntelliJ IDEA.
Created by IntelliJ IDEA.
Created by IntelliJ IDEA.
The primary UniProtAccession of a
UniProtEntry.The description annotation of the
UniProtEntry.User: Emilio Salazar Date: 25-Jun-2007
Basic interface specifying the creation of logical queries.
The factory provide a set of interfaces to create
QueryCreated 12/01/2016
CC -!- RNA EDITING: Modified_positions=x[, y, z][; Note=].
Created by IntelliJ IDEA.
Created by mkleen@ebi.ac.uk Date: 22-Oct-2007 Time: 17:02:33
Created by IntelliJ IDEA.
Created by IntelliJ IDEA.
Maximum number of match alignments reported in the result output.
A secondary UniProtAccession of a
UniProtEntry.Contains a list of all names, and respective fields, that compose a protein
within the DE line.
Encapsulates a protein sequence, in particular the sequence annotation in the
UniProtEntry and
UniParcEntry.User: Emilio Salazar Date: 14-May-2007
User: Emilio Salazar Date: 14-May-2007
User: Emilio Salazar Date: 14-May-2007
Indicate whether the sequence to blast is from DNA/RNA or a protein.
Basic service specification.
Factory specification for creating the different UniProtKB services.
Created by IntelliJ IDEA.
User: Emilio Salazar Date: 06-Jun-2007
Created by IntelliJ IDEA.
User: Emilio Salazar Date: 17-Nov-2005
Blast service geared specifically towards the UniParc blast databases.
Component used to store the most informative elements of a UniParc entry.
Created by IntelliJ IDEA.
Represents a UniParc based blast hit.
Created by IntelliJ IDEA.
One UniProtAccession of a
UniProtEntry.Blast service geared specifically towards the UniProt blast databases.
Has extra properties specific to the UniProt entry blast summary.
UniProt Component interface, returned from query component
the component types are defined in
the component types are defined in
UniProtData.ComponentTypeUniProt query result interfaces
Supported return component types
This is the Interface to the contents of a UniProt entry.
All UniProt related search fields that can be used in a
query.Represents a UniProt based blast hit.
About This Data Structure
The query builder for UniProt Service.
The main service used to query the UniProt data through
Query objects.Blast service geared specifically towards the UniRef blast databases.
Interface of the UniRef Component returned from query component
Created by IntelliJ IDEA.
Encapsulates the data found in all UniRef entries.
Represents a UniRef based blast hit.
Created by IntelliJ IDEA.
UniRefQueryBuilder class is for building a UniRef query for UniRef Services
Service to query UniRef data using a text indexed with Solr.
For unpublished observations the format of the RL line is:
RL Unpublished observations (MMM-YYYY).
A common interface used to describe object values that can be mapped to a
single String
Encapsulates the Variant Feature of a
UniProtEntry.