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Man Pages


Manual Reference Pages  -  BIO::SEQIO::FTHELPER (3)

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NAME

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

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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    :



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perl v5.20.3 BIO::SEQIO::FTHELPER (3) 2016-04-05

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