Modware::Feature

EST

   Modware::Feature::EST - Modware representation of an EST (aligned)

  do not create a Modware::Feature::EST object directly, it is for use by the Modware::Feature object

Methods description

 Title    : _get_bioperl
 Note     : creates a bioperl object representing this EST (Bio::Seq)
 Usage    : called internally by lazy evaluated 'bioperl' method 
 Function : creates a bioperl object with a location on the chromosome's bioperl object.
 Returns  : nothing
 Args     : none

 Title    : _get_cached_sequences
 Usage    : $feature->_get_cached_sequences();
 Function : gets the cached_sequences object for this feature (called from cached_sequences)
 Returns  : nothing
 Args     : none

 Title    : _init
 Note     : sets attributes specific to EST features
 Usage    : called internally by new
 Function : 
 Returns  : nothing
 Args     : none

 Title    : blast
 Function : formulates a call to private method _blast which actually runs the blast
          : and updates the database
 Returns  : nothing
 Args     : whatever '_blast' takes

Methods code

   my ($self, @args) = @_;

   my $seq = Bio::Seq->new( -seq => $self->cached_sequences->{'EST Sequence'},
                            -id  => $self->primary_id
   );

   $self->bioperl( $seq );

   my ($self) = @_;

   my $seq_hash = {};

   my $seq = $self->_database_object();
   $seq_hash->{'default'} = $seq if $seq;

   $self->cached_sequences( $seq_hash );

   my ($self, @args) = @_;

   $self->type( 'EST' );
   $self->match_type('match');

   my ($self,@args) = @_;

   $self->_database_object()->residues( $self->bioperl()->seq() );
   $self->_database_object()->seqlen( $self->bioperl()->length() );
   $self->_database_object()->update();

   my ($self, @args) = @_;


   my $sequence = $self->feature_id() ? 
                     $self->sequence( -format => 'fasta', -type => 'EST Sequence' ) :
                     $self->bioperl();

   $self->_blast( -sequence => $sequence, @args );

General documentation

   Eric Just e-just@northwestern.edu

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

 Title    : _update_cached_sequence
 Function : stores the sequence associated with this feature in the database
          : 
 Returns  : nothing
 Args     : nothing:

Copyright © 2006, Northwestern University All rights reserved.