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

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

- Constructors
- Methods to operate on files and add connectors to collection

# 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