Bio::FeatureHolderI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::FeatureHolderI - the base interface an object with features must implement

SYNOPSIS

     use Bio::SeqIO;
     # get a feature-holding object somehow: for example, Bio::SeqI objects
     # have features
     my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
     while (my $seq = $seqio->next_seq()) {
         # $seq is-a Bio::FeatureHolderI, hence:
         my @feas = $seq->get_SeqFeatures();
         # each element is-a Bio::SeqFeatureI
         foreach my $fea (@feas) {
             # do something with the feature objects
         }
     }
 
 

DESCRIPTION

This is the base interface that all feature-holding objects must implement.

Popular feature-holders are for instance Bio::Seq objects. Since Bio::SeqFeatureI defines a sub_SeqFeature() method, most Bio::SeqFeatureI implementations like Bio::SeqFeature::Generic will implement the feature holder interface as well.

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

CONTRIBUTORS

Steffen Grossmann [SG], grossman-at-molgen.mpg.de

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_SeqFeatures()

  Usage   :
  Function: Get the feature objects held by this feature holder.
  Example :
  Returns : an array of Bio::SeqFeatureI implementing objects
  Args    : none
 
 

At some day we may want to expand this method to allow for a feature filter to be passed in.

add_SeqFeature()

  Usage   : $feat->add_SeqFeature($subfeat);
            $feat->add_SeqFeature($subfeat,'EXPAND')
  Function: adds a SeqFeature into the subSeqFeature array.
            with no 'EXPAND' qualifer, subfeat will be tested
            as to whether it lies inside the parent, and throw
            an exception if not.
 
            If EXPAND is used, the parent''s start/end/strand will
            be adjusted so that it grows to accommodate the new
            subFeature
  Example :
  Returns : nothing
  Args    : a Bio::SeqFeatureI object
 
 

remove_SeqFeatures()

  Usage   : $obj->remove_SeqFeatures
  Function: Removes all sub SeqFeatures.  If you want to remove only a subset,
            remove that subset from the returned array, and add back the rest.
  Returns : The array of Bio::SeqFeatureI implementing sub-features that was
            deleted from this feature.
  Args    : none
 
 

feature_count

  Title   : feature_count
  Usage   : $obj->feature_count()
  Function: Return the number of SeqFeatures attached to a feature holder.
 
            This is before flattening a possible sub-feature tree.
 
            We provide a default implementation here that just counts
            the number of objects returned by get_SeqFeatures().
            Implementors may want to override this with a more
            efficient implementation.
 
  Returns : integer representing the number of SeqFeatures
  Args    : None
 
 

At some day we may want to expand this method to allow for a feature filter to be passed in.

Our default implementation allows for any number of additional arguments and will pass them on to get_SeqFeatures(). I.e., in order to support filter arguments, just support them in get_SeqFeatures().

get_all_SeqFeatures

  Title   : get_all_SeqFeatures
  Usage   :
  Function: Get the flattened tree of feature objects held by this
            feature holder. The difference to get_SeqFeatures is that
            the entire tree of sub-features will be flattened out.
 
            We provide a default implementation here, so implementors
            don''t necessarily need to implement this method.
 
  Example :
  Returns : an array of Bio::SeqFeatureI implementing objects
  Args    : none
 
 

At some day we may want to expand this method to allow for a feature filter to be passed in.

Our default implementation allows for any number of additional arguments and will pass them on to any invocation of get_SeqFeatures(), wherever a component of the tree implements FeatureHolderI. I.e., in order to support filter arguments, just support them in get_SeqFeatures().