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

Modware::Feature

GAP

Summary Included libraries Package variables Synopsis Description General documentation Methods
Summary
   Modware::Feature::GAP - Modware representation of a GAP
Package variables top
No package variables defined.
Included modulestop
Modware::Feature::GENERIC
Inherit top
Modware::Feature::GENERIC
Synopsistop





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





Methodstop


_initDescriptionCode


gap_typeDescriptionCode


insertDescriptionCode


newNo descriptionCode


updateNo descriptionCode





Methods description




_initcodetopprevnext


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




gap_typecodetopprevnext


 Title    : gap_type
 Usage    : print $gap->gap_type()
 Function : returns type of gap
 Returns  : string
 Args     : string ( optional )




insertcodetopprevnext


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



Methods code




_initdescriptiontopprevnext

sub _init
 {
   my ($self, @args) = @_;
   $self->type('gap');
   $self->source( "Sequencing Center" ) if (!$self->source());
}




gap_typedescriptiontopprevnext

sub gap_type
 {
   my ($self, $obj) = @_;
  #
  # fetches gap_type from database (_get_gap_type) if gap_type is not yet defined
  #  and the user is not attempting to set the gap_type options
  #
   exists $self->{gap_type} || scalar @_ > 1 || $self->gap_type( $self->_get_featureprop( 'gap type' )   );

   if(scalar @_ > 1) {
      $self->{gap_type} = $obj;
   }
   return $self->{gap_type};
}




insertdescriptiontopprevnext

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

   $self->SUPER::insert();
   $self->_insert_or_update_featureprop( 'gap type', $self->gap_type() );
}




newdescriptiontopprevnext

sub new
 {
   my ($type, @args) = @_;

   $self = $type->SUPER::new( @args );

   my @arglist = qw(
     GAP_TYPE
   );

   my ( 
      $gap_type
    )   = $self->_rearrange( [@arglist], @args );
   
   $self->gap_type( $gap_type );

   return $self;
}




updatedescriptiontopprevnext

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

   $self->SUPER::update();

   $self->_insert_or_update_featureprop( 'gap type', $self->gap_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 _