BiodbDbsInfo: A class for describing the available databases.

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

A class for describing the available databases.

Description

A class for describing the available databases.

A class for describing the available databases.

Details

The unique instance of this class is handle by the BiodbMain class and accessed through the getDbsInfo() method.

Methods

Public methods

• BiodbDbsInfo$new()

• BiodbDbsInfo$define()

• BiodbDbsInfo$getIds()

• BiodbDbsInfo$isDefined()

• BiodbDbsInfo$checkIsDefined()

• BiodbDbsInfo$get()

• BiodbDbsInfo$getAll()

• BiodbDbsInfo$print()

• BiodbDbsInfo$clone()

---

Method new()

New instance initializer. The class must not be instantiated directly. Instead, access the BiodbDbsInfo instance through the BiodbMain instance using the getDbsInfo() method.

Usage

BiodbDbsInfo$new(cfg)

Arguments

cfg

The BiodbConfig instance.

Returns

Nothing.

---

Method define()

Define databases from a structured object, normally loaded from a YAML file.

Usage

BiodbDbsInfo$define(def, package = "biodb")

Arguments

def

A named list of database definitions. The names of the list will be the IDs of the databases.

package

The package to which belong the new definitions.

Returns

Nothing.

---

Method getIds()

Gets the database IDs.

Usage

BiodbDbsInfo$getIds()

Returns

A character vector containing all the IDs of the defined databases.

---

Method isDefined()

Tests if a database is defined.

Usage

BiodbDbsInfo$isDefined(db.id)

Arguments

db.id

A database ID, as a character string.

Returns

TRUE if the specified id corresponds to a defined database, FALSE otherwise.

---

Method checkIsDefined()

Checks if a database is defined. Throws an error if the specified id does not correspond to a defined database.

Usage

BiodbDbsInfo$checkIsDefined(db.id)

Arguments

db.id

A character vector of database IDs.

Returns

Nothing.

---

Method get()

Gets information on a database.

Usage

BiodbDbsInfo$get(db.id = NULL, drop = TRUE)

Arguments

db.id

Database IDs, as a character vector. If set to NULL, informations on all databases will be returned.

drop

If TRUE and only one database ID has been submitted, returns a single BiodbDbInfo instance instead of a list.

Returns

A list of BiodbDbInfo instances corresponding to the specified database IDs.

---

Method getAll()

Gets informations on all databases.

Usage

BiodbDbsInfo$getAll()

Returns

A list of all BiodbDbInfo instances."

---

Method print()

Prints informations about this instance, listing also all databases defined.

Usage

BiodbDbsInfo$print()

Returns

Nothing.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbDbsInfo$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

BiodbMain and child class BiodbDbInfo.

Examples

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

# Getting the entry content type of a database:
db.inf <- mybiodb$getDbsInfo()$get('comp.csv.file')
cont.type <- db.inf$getPropertyValue('entry.content.type')

# Terminate instance.
mybiodb$terminate()

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