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<title>Bio::ConnectDots::DB -- Database adapter for 'connect-the-dots'</title>
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<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#author__david_burdick,_nat_goodman">AUTHOR - David Burdick, Nat Goodman</a></li>
<li><a href="#copyright">COPYRIGHT</a></li>
<li><a href="#appendix">APPENDIX</a></li>
<ul>
<li><a href="#constructors">Constructors</a></li>
<li><a href="#methods_to_manage_database">Methods to manage database</a></li>
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<h1><a name="name">NAME</a></h1>
<p>Bio::ConnectDots::DB -- Database adapter for 'connect-the-dots'</p>
<p>
</p>
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<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
use Bio::ConnectDots::DB;</pre>
<pre>
my $db=new Bio::ConnectDots::DB
(-database=>'test',-host=>'socks',-user=>'ngoodman',-password=>'secret');</pre>
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</p>
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<h1><a name="description">DESCRIPTION</a></h1>
<p>This class manages database connections and encapsulates all database
access for 'connect-the-dots'.</p>
<p>
</p>
<hr />
<h1><a name="author__david_burdick,_nat_goodman">AUTHOR - David Burdick, Nat Goodman</a></h1>
<p>Email <a href="mailto:dburdick@systemsbiology.org,">dburdick@systemsbiology.org,</a> <a href="mailto:natg@shore.net">natg@shore.net</a></p>
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<h1><a name="copyright">COPYRIGHT</a></h1>
<p>Copyright (c) 2005 Institute for Systems Biology (ISB). All Rights Reserved.</p>
<p>This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.</p>
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</p>
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<h1><a name="appendix">APPENDIX</a></h1>
<p>The rest of the documentation describes the methods.</p>
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</p>
<h2><a name="constructors">Constructors</a></h2>
<pre>
Title : new
Usage : $db=new Bio::ConnectDots::DB
(-database=>'test',-host=>'socks',-user=>'ngoodman',-password=>'secret');</pre>
<pre>
Function: Connects to database</pre>
<pre>
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</pre>
<pre>
-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</pre>
<pre>
Returns : Bio::ConnectDots::DB object</pre>
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</p>
<h2><a name="methods_to_manage_database">Methods to manage database</a></h2>
<pre>
Title : exists
Usage : print "Database exists" if $db->exists
Function: Tells whether the 'connect-the-dots' database exists
Returns : boolean</pre>
<pre>
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</pre>
<pre>
Title : create
Usage : $db->create;
Function: Create all 'connect-the-dots' tables
Returns : Nothing</pre>
<pre>
Title : analyze
Usage : $db->analyze;
Function: Run ANALYZE TABLE on all built-in 'connect-the-dots' tables
Returns : Nothing</pre>
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