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