Ewan Birney

NAME

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

SYNOPSIS

Used by Bio::SeqIO::EMBL 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://www.bioperl.org/MailList.shtml - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

Describe contact details here

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    : Bio::Seq, string indicating the source (GenBank/EMBL/SwissProt)

_parse_loc

 Title   : _parse_loc
 Usage   : $fthelper->_parse_loc( $loc_string)

 Function: Parses the given location string and returns a location object 
           with start() and end() and strand() set appropriately.
           Note that this method is private.
 Returns : location object or 0 on fail
 Args    : location string

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    :