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

- NAME
- SYNOPSIS
- DESCRIPTION
- AUTHOR - David Burdick, Nat Goodman
- COPYRIGHT
- APPENDIX

- Constructors
- Methods to manage database

# 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