LipidmapsStructureConn: Lipidmaps Structure connector class.

In pkrog/biodbLipidmaps: biodbLipidmaps, a library for connecting to the Lipidmaps Structure database

Lipidmaps Structure connector class.

Description

Lipidmaps Structure connector class.

Lipidmaps Structure connector class.

Details

Connector class for Lipidmaps Structure.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> LipidmapsStructureConn

Methods

Public methods

• LipidmapsStructureConn$wsLmsdSearch()

• LipidmapsStructureConn$wsLmsd()

• LipidmapsStructureConn$wsLmsdRecord()

• LipidmapsStructureConn$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$getSearchableFields()
• biodb::BiodbConn$initialize()
• 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 wsLmsdSearch()

Calls LMSDSearch web service. See https://www.lipidmaps.org/data/structure/programmaticaccess.html for details.

Usage

LipidmapsStructureConn$wsLmsdSearch(
  mode = NULL,
  output.mode = NULL,
  output.type = NULL,
  output.delimiter = NULL,
  output.quote = NULL,
  output.column.header = NULL,
  lmid = NULL,
  name = NULL,
  formula = NULL,
  search.type = NULL,
  smiles.string = NULL,
  exact.mass = NULL,
  exact.mass.offset = NULL,
  core.class = NULL,
  main.class = NULL,
  sub.class = NULL,
  retfmt = c("plain", "request", "parsed", "ids")
)

Arguments

mode

The search mode: 'ProcessStrSearch', 'ProcessTextSearch' or 'ProcessTextOntologySearch'. Compulsory.

output.mode

If set to 'File', will output a in format 'output.type', otherwise will output HTML.

output.type

The output format: 'TSV', 'CSV' or 'SDF'.

output.delimiter

The delimiter for TSV or CSV formats: 'Tab', 'Comma', 'Semicolon'.

output.quote

If quotes are to be used: 'Yes' or 'No'.

output.column.header

If header must be output: 'Yes' or 'No'.

lmid

a Lipidmaps ID.

name

The name to search for.

formula

The chemical formula to search for.

search.type

The search type: 'SubStructure' or 'ExactMatch'.

smiles.string

A SMILES to search for.

exact.mass

The mass to search for.

exact.mass.offset

The tolerance on the mass search.

core.class

An integer number from 1 to 8.

main.class

An integer number. See Lipidmaps documentation.

sub.class

An integer number. See Lipidmaps documentation.

retfmt

Use to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'request' will return the request that would have been sent, as a BiodbRequest object. 'parsed' will return data frame. 'ids' will return a character vector containing the IDs of the matching entries.

Returns

Depending on 'retfmt'.

---

Method wsLmsd()

Calls LMSD web service for downloading one entry.

Usage

LipidmapsStructureConn$wsLmsd(
  lmid,
  format = c("tsv", "csv"),
  retfmt = c("plain", "request", "parsed")
)

Arguments

lmid

The accession number of the entry to retrieve.

format

The output format (either 'tsv' or 'csv').

retfmt

Use to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'request' will return the request that would have been sent, as a BiodbRequest object. 'parsed' will return data frame.

Returns

Depending on 'retfmt'.

---

Method wsLmsdRecord()

Calls LMSDRecord web service. See http://www.lipidmaps.org/data/structure/programmaticaccess.html.

Usage

LipidmapsStructureConn$wsLmsdRecord(
  lmid,
  mode = NULL,
  output.type = NULL,
  output.delimiter = NULL,
  output.quote = NULL,
  output.column.header = NULL,
  retfmt = c("plain", "request", "parsed")
)

Arguments

lmid

A character vector containing the IDs of the wanted entries.

mode

If set to 'File', will output a in format 'output.type', otherwise will output HTML.

output.type

The output format: 'TSV', 'CSV' or 'SDF'.

output.delimiter

The delimiter for TSV or CSV formats: 'Tab', 'Comma', 'Semicolon'.

output.quote

If quotes are to be used: 'Yes' or 'No'.

output.column.header

If header must be output: 'Yes' or 'No'.

retfmt

Use to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'request' will return the request that would have been sent, as a BiodbRequest object. 'parsed' will return data frame.

Returns

Depending on 'retfmt'.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

LipidmapsStructureConn$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('lipidmaps.structure')

# Get an entry
e <- conn$getEntry('LMFA00000001')

# Terminate instance.
mybiodb$terminate()

pkrog/biodbLipidmaps documentation built on Dec. 1, 2022, 3:52 p.m.