MassCsvFileConn: Mass CSV File connector class.

In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases

Mass CSV File connector class.

Description

Mass CSV File connector class.

Mass CSV File connector class.

Details

This is the connector class for a MASS CSV file database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodb::CsvFileConn -> MassCsvFileConn

Methods

Public methods

• MassCsvFileConn$new()

• MassCsvFileConn$getPrecursorFormulae()

• MassCsvFileConn$isAPrecursorFormula()

• MassCsvFileConn$setPrecursorFormulae()

• MassCsvFileConn$addPrecursorFormulae()

• MassCsvFileConn$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$msmsSearch()
• biodb::BiodbConn$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()
• biodb::CsvFileConn$addField()
• biodb::CsvFileConn$getCsvQuote()
• biodb::CsvFileConn$getCsvSep()
• biodb::CsvFileConn$getFieldColName()
• biodb::CsvFileConn$getFieldNames()
• biodb::CsvFileConn$getFieldsAndColumnsAssociation()
• biodb::CsvFileConn$getUnassociatedColumns()
• biodb::CsvFileConn$hasField()
• biodb::CsvFileConn$print()
• biodb::CsvFileConn$setCsvQuote()
• biodb::CsvFileConn$setCsvSep()
• biodb::CsvFileConn$setDb()
• biodb::CsvFileConn$setField()
• biodb::CsvFileConn$setIgnoreUnassignedColumns()

---

Method new()

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

Usage

MassCsvFileConn$new(...)

Arguments

...

All parameters are passed to the super class initializer.

Returns

Nothing.

---

Method getPrecursorFormulae()

Gets the list of formulae used to recognize precursors.

Usage

MassCsvFileConn$getPrecursorFormulae()

Returns

A character vector containing chemical formulae.

---

Method isAPrecursorFormula()

Tests if a formula is a precursor formula.

Usage

MassCsvFileConn$isAPrecursorFormula(formula)

Arguments

formula

A chemical formula, as a character value.

Returns

TRUE if the submitted formula is considered a precursor.

---

Method setPrecursorFormulae()

Sets the list precursor formulae.

Usage

MassCsvFileConn$setPrecursorFormulae(formulae)

Arguments

formulae

A character vector containing formulae.

Returns

Nothing.

---

Method addPrecursorFormulae()

Adds new formulae to the list of formulae used to recognize precursors.

Usage

MassCsvFileConn$addPrecursorFormulae(formulae)

Arguments

formulae

A character vector containing formulae.

Returns

Nothing.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MassCsvFileConn$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

Super class CsvFileConn.

Examples

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

# Get path to LCMS database example file
lcmsdb <- system.file("extdata",
                      "massbank_extract_lcms_2.tsv", package="biodb")

# Create a connector
conn <- mybiodb$getFactory()$createConn('mass.csv.file', url=lcmsdb)

# Get an entry
e <- conn$getEntry('PR010001')

# Terminate instance.
mybiodb$terminate()

pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.