ExpasyEnzymeConn: Expasy ENZYME database. connector class.

In pkrog/biodbExpasy: biodbExpasy, a library for connecting to Expasy ENZYME database.

Expasy ENZYME database. connector class.

Description

Expasy ENZYME database. connector class.

Expasy ENZYME database. connector class.

Details

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.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> ExpasyEnzymeConn

Methods

Public methods

• ExpasyEnzymeConn$new()

• ExpasyEnzymeConn$wsEnzymeByName()

• ExpasyEnzymeConn$wsEnzymeByComment()

• ExpasyEnzymeConn$clone()

Inherited methods

• biodb::BiodbConnBase$getBaseUrl()

• biodb::BiodbConnBase$getConnClass()

• biodb::BiodbConnBase$getConnClassName()

• biodb::BiodbConnBase$getDbClass()

• biodb::BiodbConnBase$getEntryClass()

• biodb::BiodbConnBase$getEntryClassName()

• biodb::BiodbConnBase$getEntryContentType()

• biodb::BiodbConnBase$getEntryFileExt()

• biodb::BiodbConnBase$getEntryIdField()

• biodb::BiodbConnBase$getName()

• biodb::BiodbConnBase$getPropSlots()

• biodb::BiodbConnBase$getPropValSlot()

• biodb::BiodbConnBase$getPropertyValue()

• biodb::BiodbConnBase$getSchedulerNParam()

• biodb::BiodbConnBase$getSchedulerTParam()

• biodb::BiodbConnBase$getToken()

• biodb::BiodbConnBase$getUrl()

• biodb::BiodbConnBase$getUrls()

• biodb::BiodbConnBase$getWsUrl()

• biodb::BiodbConnBase$getXmlNs()

• biodb::BiodbConnBase$hasProp()

• biodb::BiodbConnBase$hasPropSlot()

• biodb::BiodbConnBase$isSlotProp()

• biodb::BiodbConnBase$propExists()

• biodb::BiodbConnBase$setBaseUrl()

• biodb::BiodbConnBase$setPropValSlot()

• biodb::BiodbConnBase$setPropertyValue()

• biodb::BiodbConnBase$setSchedulerNParam()

• biodb::BiodbConnBase$setSchedulerTParam()

• biodb::BiodbConnBase$setToken()

• biodb::BiodbConnBase$setUrl()

• biodb::BiodbConnBase$setWsUrl()

• biodb::BiodbConnBase$updatePropertiesDefinition()

• biodb::BiodbConn$addNewEntry()

• biodb::BiodbConn$allowEditing()

• biodb::BiodbConn$allowWriting()

• biodb::BiodbConn$annotateMzValues()

• biodb::BiodbConn$checkDb()

• biodb::BiodbConn$collapseResultsDataFrame()

• biodb::BiodbConn$correctIds()

• biodb::BiodbConn$deleteAllCacheEntries()

• biodb::BiodbConn$deleteAllEntriesFromPersistentCache()

• biodb::BiodbConn$deleteAllEntriesFromVolatileCache()

• biodb::BiodbConn$deleteWholePersistentCache()

• biodb::BiodbConn$disallowEditing()

• biodb::BiodbConn$disallowWriting()

• biodb::BiodbConn$download()

• biodb::BiodbConn$editingIsAllowed()

• biodb::BiodbConn$filterEntriesOnRt()

• biodb::BiodbConn$getAllCacheEntries()

• biodb::BiodbConn$getAllVolatileCacheEntries()

• biodb::BiodbConn$getBiodb()

• biodb::BiodbConn$getCacheFile()

• biodb::BiodbConn$getCacheId()

• biodb::BiodbConn$getChromCol()

• biodb::BiodbConn$getDownloadPath()

• biodb::BiodbConn$getEntry()

• biodb::BiodbConn$getEntryContent()

• biodb::BiodbConn$getEntryContentFromDb()

• biodb::BiodbConn$getEntryContentRequest()

• biodb::BiodbConn$getEntryIds()

• biodb::BiodbConn$getEntryImageUrl()

• biodb::BiodbConn$getEntryPageUrl()

• biodb::BiodbConn$getId()

• biodb::BiodbConn$getMatchingMzField()

• biodb::BiodbConn$getMzValues()

• biodb::BiodbConn$getNbEntries()

• biodb::BiodbConn$getNbPeaks()

• biodb::BiodbConn$getSearchableFields()

• biodb::BiodbConn$isCompounddb()

• biodb::BiodbConn$isDownloadable()

• biodb::BiodbConn$isDownloaded()

• biodb::BiodbConn$isEditable()

• biodb::BiodbConn$isExtracted()

• biodb::BiodbConn$isMassdb()

• biodb::BiodbConn$isRemotedb()

• biodb::BiodbConn$isSearchableByField()

• biodb::BiodbConn$isWritable()

• biodb::BiodbConn$makeRequest()

• biodb::BiodbConn$makesRefToEntry()

• biodb::BiodbConn$msmsSearch()

• biodb::BiodbConn$print()

• biodb::BiodbConn$requiresDownload()

• biodb::BiodbConn$searchByName()

• biodb::BiodbConn$searchCompound()

• biodb::BiodbConn$searchForEntries()

• biodb::BiodbConn$searchForMassSpectra()

• biodb::BiodbConn$searchMsEntries()

• biodb::BiodbConn$searchMsPeaks()

• biodb::BiodbConn$searchMzRange()

• biodb::BiodbConn$searchMzTol()

• biodb::BiodbConn$setDownloadedFile()

• biodb::BiodbConn$setEditingAllowed()

• biodb::BiodbConn$setMatchingMzField()

• biodb::BiodbConn$setWritingAllowed()

• biodb::BiodbConn$write()

• biodb::BiodbConn$writingIsAllowed()

---

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage

ExpasyEnzymeConn$new(...)

Arguments

...

All parameters are passed to the super class initializer.

Returns

Nothing.

---

Method wsEnzymeByName()

Calls enzyme-byname web service and returns the HTML result. See http://enzyme.expasy.org/enzyme-byname.html.

Usage

ExpasyEnzymeConn$wsEnzymeByName(
  name,
  retfmt = c("plain", "request", "parsed", "ids")
)

Arguments

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.

Returns

Depending on retfmt.

---

Method wsEnzymeByComment()

Calls enzyme-bycomment web service and returns the HTML result. See http://enzyme.expasy.org/enzyme-bycomment.html.

Usage

ExpasyEnzymeConn$wsEnzymeByComment(
  comment,
  retfmt = c("plain", "request", "parsed", "ids")
)

Arguments

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.

Returns

Depending on retfmt.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ExpasyEnzymeConn$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

BiodbConn.

Examples

# 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()

pkrog/biodbExpasy documentation built on March 29, 2022, 9:52 a.m.