Modware::Feature

GENERIC

   Modware::Feature::GENERIC - default Modware representation of a simple genome sequence feature (start, stop, strand)

     my $tata_box = new Modware::Feature(
	     -type              => 'TATA_box',
		 -source            => 'test source',
		 -bioperl           => $some_bio_seqFeature_generic_object,
		 -reference_feature => $some_chromosome_or_contig_object
	  );

      # or 
      my $tata_box = new Modware::Feature( -primary_id => $id_of_some_tatabox_feature );

      # since there is no Modware::Feature::TATA_BOX class a Modware::Feature::Generic class
      # will get created

   Generic feature class.  Used for simple features with a start, stop, stop and no structure.
   This default feature class is instantiated when Modware encounters a feature with a 'type'
   that does not map to a class in Modware::Feature::*

   The assumption is that the feature type can be represented by a Bio::SeqFeature::Generic object 
   (start, stop, strand, refernece feature)

Methods description

 Title    : _get_bioperl
 Note     : creates a bioperl object representing this Contig (Bio::SeqFeature::Generic)
 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    : _init
 Usage    : called internally by constructor
          : (hook to do any post-instantiation initialization)
 Function : does nothing in Modware::Feature::GENERIC
 Returns  : nothing
 Args     : none

 Title    : _update_cached_sequence
 Note     : internal method for features that store sequences
 Function : do not store sequences for generic features, does nothing here
 Returns  : nothing
 Args     : none

 Title    : end
 Function : returns the end position relatve to a genomic
          : reference feature (chromosome, contig, etc.)
 Returns  : integer base position 
 Args     : none

 Title    : insert
 Function : calls SUPER::insert but then inserts the location 
          : 
 Returns  : nothing
 Args     : none

 Title    : length
 Function : returns the length of the feature
 Returns  : integer length
 Args     : none

 Title    : new
 Note     : never call this directly. Use new Modware::Feature with 'type' set to '
         
 Usage    : my $match = new Modware::Feature(
			   -type    => 'match',
			   -source  => 'blastn.10.19.2007',
			   -bioperl => $some_bio_search_hit_generichit_object
	        );
 Function : called by Modware::Feature->new when type = 'match'
 Returns  : feature_id string
 Args     : named arguments: -source, -type, -bioperl (Bio::Search::Hit::GenericHit), -description

 Title    : shift_feature
 Note     : 
 Usage    : To move a feature upstream by 125 bases:
          : $feature->shift_feature( 25 );
 Function : moves a feature by a specified amount
 Returns  : nothing
 Args     : integer ( + or - )

 Title    : start
 Function : returns the start position relatve to a genomic
          : reference feature (chromosome, contig, etc.)
 Returns  : integer base position 
 Args     : none

 Title    : update
 Function : calls SUPER::update but then updates the location
          : 
 Returns  : nothing
 Args     : none

Methods code

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

   my $bioperl  = new Bio::SeqFeature::Generic();

   $bioperl->start( $self->_featureloc() + 1 );
   $bioperl->end( $self->_featureloc() );
   $bioperl->strand( $self->_featureloc() ) if $self->_featureloc();

   $bioperl->primary_tag( $self->type() );
   $self->reference_feature();
  #
  # returning a CONTIG object having a chromosome attached to it
  #   to chromosome ( in _get_contig_features()  )
  #   results in weird behavior: if there are more than 8 contigs in the
  #   array the code breaks, but does not throw an error.  
  #
   $bioperl->attach_seq( $self->reference_feature()->bioperl ) if $self->{'reference_feature'};


   $self->bioperl( $bioperl );

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

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

  #
  # not updateing any seqs
  #

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

   return $self->bioperl(@args);

   my ($self,  @args) = @_;
   $self->SUPER::insert();
   $self->_insert_featureloc();

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

   return $self->bioperl(@args);

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

  #
  #  do not bless it here, assume subclass will bless as a subclass type
  #
   my $self = {};
   bless $self,$type;

   # You can pass in a chromosome_name or a reference _feature
   # chromosome_name will probably be deprecated
   my @arglist = qw(
     SOURCE DESCRIPTION CHROMOSOME_NAME START END REFERENCE_FEATURE
   );

   my ( 
     $source, $description, $chromosome_name, $start, $end, $reference_feature
    )   = $self->_rearrange( [@arglist], @args );



   if ( !($chromosome_name xor $reference_feature)|| !$start || !$end ) {
      $self->throw( "Need -start, -end, and -chromosome_name or -reference_feature arguements to constructor.");
   }
   my $bioperl            = new Bio::SeqFeature::Generic( -start => $start, -end => $end );
   $reference_feature     =  new Modware::Chromosome( -name => $chromosome_name ) if $chromosome_name;

   $self->source            ( $source            ) if defined $source;
   $self->bioperl           ( $bioperl           ) if defined $bioperl;
   $self->description       ( $description       ) if defined $description;
   $self->reference_feature ( $reference_feature ) if defined $reference_feature;

   $bioperl->attach_seq( $self->reference_feature->bioperl ) if $self->{'reference_feature'};

   $self->qualifiers( [] );
   $self->_init();
   return $self;

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

   my $bioperl = $self->bioperl;
   $bioperl->start(  $bioperl->start() + $offset   );
   $bioperl->end  (  $bioperl->end()   + $offset   );

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

   return $self->bioperl(@args);

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

   $self->SUPER::update();
   
   if (  $self->{'bioperl'} ) {
      $self->_update_featureloc();
   }

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 _

Copyright © 2006, Northwestern University All rights reserved.