/ 
bioperl-1.0.2
/ Bio::SeqIO::FTHelper

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    :