MassCsvFileConn {biodb} | R Documentation

## 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$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$isSearchableByField()`

- `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()

[Package biodb version 1.2.2 Index]