David Burdick > Bio-ConnectDots > Bio::ConnectDots::ConnectorSet

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ConnectDots/Bio-ConnectDots-1.0.2.tar.gz

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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
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