BiodbEntryFields: A class for handling description of all entry fields.
In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases
BiodbEntryFields R Documentation
A class for handling description of all entry fields.
Description
A class for handling description of all entry fields.
A class for handling description of all entry fields.
Details
The unique instance of this class is handle by the BiodbMain
class and accessed through the getEntryFields() method.
Methods
Public methods
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Method new()
New instance initializer. No BiodbEntryFields instance must be created
directly. Instead, call the getEntryFields() method of BiodbMain.
Usage
BiodbEntryFields$new(parent)
Arguments
parentThe BiodbMain instance.
Returns
Nothing.
Method notifyCfgUpdate()
Call back method called when a value is modified inside the configuration.
Usage
BiodbEntryFields$notifyCfgUpdate(k, v)
Arguments
kThe config key name.
vThe value associated with the key.
Returns
Nothing.
Method isAlias()
Tests if names are aliases.
Usage
BiodbEntryFields$isAlias(name)
Arguments
nameA character vector of names or aliases to test.
Returns
A logical vector, the same length as name, with TRUE
for name values that are an alias of a field, and FALSE otherwise."
Method formatName()
Format field name(s) for biodb format: set to lower case and remove
dot or underscore characters depending on configuration.
Usage
BiodbEntryFields$formatName(name)
Arguments
nameA character vector of names or aliases to test.
Returns
A character vector of formatted names.
Method isDefined()
Tests if names are defined fields.
Usage
BiodbEntryFields$isDefined(name)
Arguments
nameA character vector of names or aliases to test.
Returns
A logical vector, the same length as name, with TRUE
for name values that corresponds to a defined field.
Method checkIsDefined()
Tests if names are valid defined fields. Throws an error if any name
does not correspond to a defined field.
Usage
BiodbEntryFields$checkIsDefined(name)
Arguments
nameA character vector of names or aliases to test.
Returns
Nothing.
Method getRealName()
Gets the real names (main names) of fields. If some name is not found
neither in aliases nor in real names, an error is thrown.
Usage
BiodbEntryFields$getRealName(name, fail = TRUE)
Arguments
nameA character vector of names or aliases.
failFails if name is unknown.
Returns
A character vector, the same length as name, with the real
field name for each name given (i.e. each alias is replaced with the
real name).
Method get()
Gets a BiodbEntryField instance.
Usage
BiodbEntryFields$get(name, drop = TRUE)
Arguments
nameA character vector of names or aliases.
dropIf TRUE and only one name has been submitted, returns a
single BiodbEntryField instance instead of a list.
Returns
A named list of BiodbEntryField instances. The names of the
list are the real names of the entry fields, thus they may be
different from the one provided inside the name argument.
Method getFieldNames()
Gets the main names of all fields.
Usage
BiodbEntryFields$getFieldNames(type = NULL, computable = NULL)
Arguments
typeSet this parameter to a character vector in order to
return only the names of the fields corresponding to the types
specified.
computableIf set to TRUE, returns only the names of computable
fields. If set to FALSE, returns only the names of fields that are not
computable.
Returns
A character vector containing all selected field names.
Method getDatabaseIdField()
Gets a database ID field.
Usage
BiodbEntryFields$getDatabaseIdField(database)
Arguments
databaseThe name (i.e.: Biodb ID) of a database.
Returns
accession numbers) for this database.
Method print()
Prints information about the instance.
Usage
BiodbEntryFields$print()
Returns
Nothing.
Method define()
Defines fields.
Usage
BiodbEntryFields$define(def)
Arguments
defA named list of field definitions. The names of the list are the
main names of the fields.
Returns
Nothing.
Method terminate()
Terminates the instance. This method will be called
automatically by the BiodbMain instance when you call
Usage
BiodbEntryFields$terminate()
Arguments
BiodbMain:terminate().
Returns
Nothing.
Method clone()
The objects of this class are cloneable with this method.
Usage
BiodbEntryFields$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
BiodbMain and child class
BiodbEntryField.
Examples
# Getting information about the accession field:
mybiodb <- biodb::newInst()
entry.field <- mybiodb$getEntryFields()$get('accession')
# Test if a name is an alias of a field
mybiodb$getEntryFields()$isAlias('genesymbols')
# Test if a name is associated with a defined field
mybiodb$getEntryFields()$isDefined('name')
# Terminate instance.
mybiodb$terminate()
pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.
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| BiodbEntryFields | R Documentation |
A class for handling description of all entry fields.
Description
A class for handling description of all entry fields.
A class for handling description of all entry fields.
Details
The unique instance of this class is handle by the BiodbMain
class and accessed through the getEntryFields() method.
Methods
Public methods
Method new()
New instance initializer. No BiodbEntryFields instance must be created directly. Instead, call the getEntryFields() method of BiodbMain.
Usage
BiodbEntryFields$new(parent)
Arguments
parentThe BiodbMain instance.
Returns
Nothing.
Method notifyCfgUpdate()
Call back method called when a value is modified inside the configuration.
Usage
BiodbEntryFields$notifyCfgUpdate(k, v)
Arguments
kThe config key name.
vThe value associated with the key.
Returns
Nothing.
Method isAlias()
Tests if names are aliases.
Usage
BiodbEntryFields$isAlias(name)
Arguments
nameA character vector of names or aliases to test.
Returns
A logical vector, the same length as name, with TRUE
for name values that are an alias of a field, and FALSE otherwise."
Method formatName()
Format field name(s) for biodb format: set to lower case and remove dot or underscore characters depending on configuration.
Usage
BiodbEntryFields$formatName(name)
Arguments
nameA character vector of names or aliases to test.
Returns
A character vector of formatted names.
Method isDefined()
Tests if names are defined fields.
Usage
BiodbEntryFields$isDefined(name)
Arguments
nameA character vector of names or aliases to test.
Returns
A logical vector, the same length as name, with TRUE
for name values that corresponds to a defined field.
Method checkIsDefined()
Tests if names are valid defined fields. Throws an error if any name does not correspond to a defined field.
Usage
BiodbEntryFields$checkIsDefined(name)
Arguments
nameA character vector of names or aliases to test.
Returns
Nothing.
Method getRealName()
Gets the real names (main names) of fields. If some name is not found neither in aliases nor in real names, an error is thrown.
Usage
BiodbEntryFields$getRealName(name, fail = TRUE)
Arguments
nameA character vector of names or aliases.
failFails if name is unknown.
Returns
A character vector, the same length as name, with the real
field name for each name given (i.e. each alias is replaced with the
real name).
Method get()
Gets a BiodbEntryField instance.
Usage
BiodbEntryFields$get(name, drop = TRUE)
Arguments
nameA character vector of names or aliases.
dropIf TRUE and only one name has been submitted, returns a single BiodbEntryField instance instead of a list.
Returns
A named list of BiodbEntryField instances. The names of the list are the real names of the entry fields, thus they may be different from the one provided inside the name argument.
Method getFieldNames()
Gets the main names of all fields.
Usage
BiodbEntryFields$getFieldNames(type = NULL, computable = NULL)
Arguments
typeSet this parameter to a character vector in order to return only the names of the fields corresponding to the types specified.
computableIf set to TRUE, returns only the names of computable fields. If set to FALSE, returns only the names of fields that are not computable.
Returns
A character vector containing all selected field names.
Method getDatabaseIdField()
Gets a database ID field.
Usage
BiodbEntryFields$getDatabaseIdField(database)
Arguments
databaseThe name (i.e.: Biodb ID) of a database.
Returns
accession numbers) for this database.
Method print()
Prints information about the instance.
Usage
BiodbEntryFields$print()
Returns
Nothing.
Method define()
Defines fields.
Usage
BiodbEntryFields$define(def)
Arguments
defA named list of field definitions. The names of the list are the main names of the fields.
Returns
Nothing.
Method terminate()
Terminates the instance. This method will be called automatically by the BiodbMain instance when you call
Usage
BiodbEntryFields$terminate()
Arguments
BiodbMain:terminate().
Returns
Nothing.
Method clone()
The objects of this class are cloneable with this method.
Usage
BiodbEntryFields$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
BiodbMain and child class
BiodbEntryField.
Examples
# Getting information about the accession field:
mybiodb <- biodb::newInst()
entry.field <- mybiodb$getEntryFields()$get('accession')
# Test if a name is an alias of a field
mybiodb$getEntryFields()$isAlias('genesymbols')
# Test if a name is associated with a defined field
mybiodb$getEntryFields()$isDefined('name')
# Terminate instance.
mybiodb$terminate()
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