Bio::SeqIO::FTHelper(3User Contributed Perl DocumentatiBio::SeqIO::FTHelper(3)NAMEBio::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 :
perl v5.14.1 2011-07-22 Bio::SeqIO::FTHelper(3)
