15 Apr 2011 19:35:57 UTC
- Distribution: BioPerl-DB
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- License: perl_5
- Perl: v5.6.1
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- This version
- Latest versionCJFIELDS Christopher Fieldsand 1 contributors
- BioPerl Team
- AUTHOR - Hilmar Lapp
Bio::DB::DBI.pm - DESCRIPTION of Interface
Give standard usage here
Describe the interface here
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Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
Email hlapp at gmx.net
Describe contact details here
Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_id_value Usage : $pk = $obj->next_id_value("bioentry"); Function: Returns the next unique primary key value. Depending on the argument and the driver, the value may not be unique between tables. Example : Returns : a value suitable for use as a primary key Args : The database connection handle to use for retrieving the next primary key value. Optionally, the name of the primary key generating sequence. The driver is not required to honor the argument if present.
Title : last_id_value Usage : Function: Returns the last unique primary key value allocated. Depending on the argument and the driver, the value may be specific to a table, or independent of the table. Example : Returns : a value suitable for use as a primary key Args : The database connection handle to use for retrieving the primary key from the last insert. An individual driver may allow this argument to be omitted if next_id_value() was called before for obtaining the primary key value. Optionally, the name of the primary key generating sequence. The driver is not required to honor the argument if present.
Title : nvl_sqlfunc Usage : Function: Get the name of the SQL function that takes two arguments and returns the first if it is not null, and the second otherwise. Most RDBMSs will have such a function, but unfortunately the naming is different between them. E.g., in MySQL the name is IFNULL(), whereas in Oracle it is NVL(). Example : Returns : the name of the function as a string, without parentheses Args : none
Title : get_connection Usage : Function: Obtains a connection handle to the database represented by the the DBContextI object, passing additional args to the DBI->connect() method if a new connection is created. Contrary to new_connection(), this method may return shared connections from a pool. The implementation should make sure though that the returned handle was opened with the given parameters. In addition, the caller must not disconnect the obtained handle deliberately. Instead, the implementing object will disconnect and dispose of open handles once it is being garbage collected, or once disconnect() is called with the same or no parameters. Example : Returns : an open DBI database handle Args : A Bio::DB::DBContextI implementing object. Additional hashref parameter to be passed to DBI->connect() in case of a new connection.
Title : new_connection Usage : Function: Obtains a new connection handle to the database represented by the the DBContextI object, passing additional args to the DBI->connect() method. This method is supposed to always open a new connection. Also, the implementing class is expected to release proper disconnection of the handle entirely to the caller. Example : Returns : an open DBI database handle Args : A Bio::DB::DBContextI implementing object. Additional hashref parameter to pass to DBI->connect().
Title : disconnect Usage : Function: Disconnects all or a certain number of connections matching the parameters. The connections affected are those previously obtained through get_connection() (shared connections from a pool). Example : Returns : none Args : Optionally, a Bio::DB::DBContextI implementing object. Additional hashref parameter with settings that were passed to get_connection().
Title : conn_params Usage : $dbi->conn_params($requestor, $newval) Function: Gets/sets connection parameters suitable for the specific driver and the specific requestor. A particular implementation may choose to ignore the requestor, but it may also use it to return different parameters, based on, e.g., which interface the requestor implements. Usually the caller will pass $self as the value for $requestor, but an implementation is is expected to accept a class or interface name as well. If an object is passed for $requestor, the implementation is expected to return parameters for an interface the object implements, or for a parent class, whichever comes first, and provided no parameters have been set specifically for the class of the passed object. This makes is possible, as an example, to set parameters for Bio::DB::PersistenceAdaptorI, and have those returned for every object that implements that interface. Example : Returns : a hashref to be passed to get_connection() or new_connection() (which would pass it on to DBI->connect()). Args : The requesting object, or alternatively its class name or interface. Optionally, on set the new value (which must be undef or a hashref).
Module Install Instructions
To install Bio::BioEntry, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::BioEntry
For more information on module installation, please visit the detailed CPAN module installation guide.