Christopher Fields > BioPerl-1.6.921 > Bio::SeqIO::FTHelper

Download:
BioPerl-1.6.921.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.924

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:

  https://redmine.open-bio.org/projects/bioperl/

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    :
syntax highlighting: