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Bio::SeqIO::FTHelper.3pm

NAME

Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables

SYNOPSIS

Used by Bio::SeqIO::EMBL,Bio::SeqIO::genbank, and Bio::SeqIO::swiss to help process the Feature Table

DESCRIPTION

Represents one particular Feature with the following fields

       key - the key of the feature
       loc - the location string of the feature
       <other fields> - other fields
 
 

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

CONTRIBUTORS

Jason Stajich jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_generic_seqfeature

  Title   : _generic_seqfeature
  Usage   : $fthelper->_generic_seqfeature($annseq, "GenBank")
  Function: processes fthelper into a generic seqfeature
  Returns : TRUE on success and otherwise FALSE
  Args    : The Bio::Factory::LocationFactoryI object to use for parsing
            location strings. The ID (e.g., display_id) of the sequence on which
            this feature is located, optionally a string indicating the source
            (GenBank/EMBL/SwissProt)
 
 

from_SeqFeature

  Title   : from_SeqFeature
  Usage   : @fthelperlist = Bio::SeqIO::FTHelper::from_SeqFeature($sf,
                                                      $context_annseq);
  Function: constructor of fthelpers from SeqFeatures
          :
          : The additional annseq argument is to allow the building of FTHelper
          : lines relevant to particular sequences (ie, when features are spread over
          : enteries, knowing how to build this)
  Returns : an array of FThelpers
  Args    : seq features
 
 

key

  Title   : key
  Usage   : $obj->key($newval)
  Function:
  Example :
  Returns : value of key
  Args    : newvalue (optional)
 
 

loc

  Title   : loc
  Usage   : $obj->loc($newval)
  Function:
  Example :
  Returns : value of loc
  Args    : newvalue (optional)
 
 

field

  Title   : field
  Usage   :
  Function:
  Example :
  Returns :
  Args    :
 
 

add_field

  Title   : add_field
  Usage   :
  Function:
  Example :
  Returns :
  Args    :