NAME

Bio::ConnectDots::DB -- Database adapter for 'connect-the-dots'

SYNOPSIS

use Bio::ConnectDots::DB;

my $db=new Bio::ConnectDots::DB
  (-database=>'test',-host=>'socks',-user=>'ngoodman',-password=>'secret');

DESCRIPTION

This class manages database connections and encapsulates all database access for 'connect-the-dots'.

AUTHOR - David Burdick, Nat Goodman

Email dburdick@systemsbiology.org, natg@shore.net

COPYRIGHT

Copyright (c) 2005 Institute for Systems Biology (ISB). All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

APPENDIX

The rest of the documentation describes the methods.

Constructors

Title   : new
Usage   : $db=new Bio::ConnectDots::DB
            (-database=>'test',-host=>'socks',-user=>'ngoodman',-password=>'secret');

Function: Connects to database

Args    : -database => name of PostgreSQL database to use
          -host => hostname of PostgreSQL database server
          -server => synonym for host
          -user => name of PostgreSQL user
          -password => password of PostgreSQL user

          -ext_directory => directory for temporary files used for loading and fetching data
             default /usr/tmp/<user>, eg, /usr/tmp/ngoodman
          -load_save => controls whether load files are saved after use.  Helpful
             for debugging
             default - files not saved
             'all' -- files are saved
             'last' -- only last file is saved
          -load_chunksize => number of Dots loaded at a time.  Tuning parameter.
             default 100000

Returns : Bio::ConnectDots::DB object

Methods to manage database

Title   : exists
Usage   : print "Database exists" if $db->exists
Function: Tells whether the 'connect-the-dots' database exists
Returns : boolean

Title   : drop
Usage   : $db->drop;
Function: Drop all 'connect-the-dots' tables
Returns : Nothing
Note    : Only drops the built-in tables, not the ones created by queries

Title   : create
Usage   : $db->create;
Function: Create all 'connect-the-dots' tables
Returns : Nothing

Title   : analyze
Usage   : $db->analyze;
Function: Run ANALYZE TABLE on all built-in 'connect-the-dots' tables
Returns : Nothing