NAME

Bio::ConnectDots::ConnectorSet -- 'connect-the-dots'

SYNOPSIS

  use Bio::ConnectDots::DB;
  use Bio::ConnectDots::ConnectorSet;

  my $db=new Bio::ConnectDots::DB(-database=>'test',
                                       -host=>'servername',
                                       -user=>'username',
                                       -password=>'secret');
  my $connectorset=new Bio::ConnectDots::ConnectorSet(
                     -name=>'LocusLink',
                     -module=>'LocusLink',
                     -db=>$db,
                     -file=>'LL_tmpl',
                     -dotsets=>['LocusLink','UniGene','Organism',
                               {'PreferedSymbol'=>'Gene Symbol','Alias Symbol'=>'Gene Symbol','Hugo'=>'Gene Name'}]
									    );
  $connectorset->load_file;

DESCRIPTION

This class represents a data source, such as LocusLink, that contain connection information 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   : $connector_set=new Bio::ConnectDots::ConnectorSet(
                           -name=>'LocusLink',
                           -module=>'LocusLink',
                           -db=>$db,
                           -file=>'LL_tmpl',
                           -dotsets=>['LocusLink','UniGene','Organism',
                                     {'PreferedSymbol'=>'Gene Symbol','Alias Symbol'=>'Gene Symbol',
                                      'Hugo'=>'Gene Name'}]
                            );
Function: Create ConnectorSet object, typically for parsing and loading a file
          into the database

Args    : -name => name of ConnectorSet
          -module => subclass module to be loaded. The '.pm' for this module must
             be in a directory Bio/ConnectDots/ConnectorSet beneath one of
             your PERL5LIBs
          -db => Bio::ConnectDots::DB object connected to database
          -file => name of file to be loaded
          -dotsets => ARRAY of DotSet names or HASH of label=>name. In the first
             case, ie, if no label is given, the name is used as the label

          -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

          The following arguments are set internally:

          -db_id => database id for ConnectorSet object
          -saved_file => name of file loaded when object created

Returns : Object whose class is a subclass of Bio::ConnectDots::ConnectorSet
         determined by -module

Methods to operate on files and add connectors to collection

Title   : load_file
Usage   : $connectorset->load_file;
Function: Parse entries and load into database
Returns : Nothing

Title   : parse_file
Usage   : $connectorset->parse_file;
Function: Parse entries into 'instance' objects and store in object
Returns : Nothing

Title   : put_dot
Usage   : $connectorset->put_dot('Hugo','CASP7')
Function: Add a dot to the 'current' Connector. Used in parse_entry methods
Args    : label of DotSet
          Dot value, ie, an actual identifier
Returns : ARRAY of values for the label