Title: | biodbExpasy, a library for connecting to Expasy ENZYME database. |
---|---|
Description: | The biodbExpasy library provides access to Expasy ENZYME database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or comments. |
Authors: | Pierrick Roger [aut, cre] |
Maintainer: | Pierrick Roger <[email protected]> |
License: | AGPL-3 |
Version: | 1.9.0 |
Built: | 2024-06-30 02:57:04 UTC |
Source: | https://github.com/bioc/biodbExpasy |
The biodbExpasy library provides access to Expasy ENZYME database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or comments.
See vignette biodbExpasy:
vignette('biodbExpasy', package='biodbExpasy')
Maintainer: Pierrick Roger [email protected] (ORCID)
Expasy ENZYME database. connector class.
Expasy ENZYME database. connector class.
Connector class for Expasy ENZYME database.
This is a concrete connector class. It must never be instantiated directly,
but instead be instantiated through the factory BiodbFactory
.
Only specific methods are described here. See super classes for the
description of inherited methods.
biodb::BiodbConnBase
-> biodb::BiodbConn
-> ExpasyEnzymeConn
new()
New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.
ExpasyEnzymeConn$new(...)
...
All parameters are passed to the super class initializer.
Nothing.
wsEnzymeByName()
Calls enzyme-byname web service and returns the HTML result. See http://enzyme.expasy.org/enzyme-byname.html.
ExpasyEnzymeConn$wsEnzymeByName( name, retfmt = c("plain", "request", "parsed", "ids") )
name
The name to search for.
retfmt
The format to use for the returned value. 'plain' will return the raw result from the server, as a character value. 'request' will return a BiodbRequest instance containing the request as it would have been sent. 'parsed' will return an XML object, containing the parsed result. 'ids' will return a character vector containing the IDs of the matching entries.
Depending on retfmt
.
wsEnzymeByComment()
Calls enzyme-bycomment web service and returns the HTML result. See http://enzyme.expasy.org/enzyme-bycomment.html.
ExpasyEnzymeConn$wsEnzymeByComment( comment, retfmt = c("plain", "request", "parsed", "ids") )
comment
The comment to search for.
retfmt
The format to use for the returned value. 'plain' will return the raw result from the server, as a character value. 'request' will return a BiodbRequest instance containing the request as it would have been sent. 'parsed' will return an XML object, containing the parsed result. 'ids' will return a character vector containing the IDs of the matching entries.
Depending on retfmt
.
clone()
The objects of this class are cloneable with this method.
ExpasyEnzymeConn$clone(deep = FALSE)
deep
Whether to make a deep clone.
# Create an instance with default settings: mybiodb <- biodb::newInst() # Get a connector: conn <- mybiodb$getFactory()$createConn('expasy.enzyme') # Get the first entry e <- conn$getEntry('1.1.1.1') # Terminate instance. mybiodb$terminate()
# Create an instance with default settings: mybiodb <- biodb::newInst() # Get a connector: conn <- mybiodb$getFactory()$createConn('expasy.enzyme') # Get the first entry e <- conn$getEntry('1.1.1.1') # Terminate instance. mybiodb$terminate()
Entry class for Expasy ENZYME database.
biodb::BiodbEntry
-> biodb::BiodbTxtEntry
-> ExpasyEnzymeEntry
clone()
The objects of this class are cloneable with this method.
ExpasyEnzymeEntry$clone(deep = FALSE)
deep
Whether to make a deep clone.
# Create an instance with default settings: mybiodb <- biodb::newInst() # Get a connector that inherits from ExpasyEnzymeConn: conn <- mybiodb$getFactory()$createConn('expasy.enzyme') # Get the first entry e <- conn$getEntry('1.1.1.1') # Terminate instance. mybiodb$terminate()
# Create an instance with default settings: mybiodb <- biodb::newInst() # Get a connector that inherits from ExpasyEnzymeConn: conn <- mybiodb$getFactory()$createConn('expasy.enzyme') # Get the first entry e <- conn$getEntry('1.1.1.1') # Terminate instance. mybiodb$terminate()