These documents are For the HEAD of the CVS repository on July 19, 2007 Api docs for previous releases

Modware::Feature

NCRNA

Summary Included libraries Package variables Synopsis Description General documentation Methods
Summary
   Modware::Feature::NCRNA -  Modware representation of an ncRNA (non-coding RNA)
Package variables top
Privates (from my definitions)
$display_types = { 'C_D_box_snoRNA' => 'C/D box snoRNA', 'H_ACA_box_snoRNA' => 'H/ACA box snoRNA'}
Included modulestop
Modware::Feature::TRANSCRIPT
Inherit top
Modware::Feature::TRANSCRIPT
Synopsistop
  NEVER INSTANTIATE THIS OBJECT, USE Modware::Feature

  USE CASE : print the spliced transcript sequence stored in the database as a fasta file
     my $feature = new Modware::Feature( -primary_id => 'DDB0191090' );
     print $feature->sequence( -type => 'spliced_transcript', -format => 'fasta' );
Descriptiontop
   An ncRNA feature is a generic high level term for any RNA feature that does not code for a protein
   and IS NOT A tRNA (which have their own class).  At the current time, all of these features behave
   the same and no particular behavior is added into this class.  It is simply a concrete implementation
   of the abstract class Modware::Feature::TRANSCRIPT

   The bioperl representation of this feature type is the same as the default for transcripts:
   A Bio::SeqFeature::Generic object with Bio::SeqFeature::Generic subfeatures.
Methodstop
_initDescriptionCode

Methods description

_initcodetopprevnext
 Title : _init
 Note : sets the display type for this feature
 Usage : called internally by new
 Function :
 Returns : nothing
 Args : none

Methods code

_initdescriptiontopprevnext
sub _init {
   my ($self, @args) = @_;

   $self->SUPER::_init( @args );

   my $display_type = $display_types->{$self->type()} || $self->type();
  
   $display_type =~ s/_/ /g;
   $self->display_type( $display_type ) if $display_type;
}

General documentation

AUTHOR - Eric Just top
   Eric Just e-just@northwestern.edu
APPENDIX top
   The rest of the documentation details each of the object
   methods. Internal methods are usually preceded with a _