[Bioperl-l] code reuse with moose

[Siddhartha Basu]

Putting it in the bioperl list,  makes more sense here, 

On Wed, 12 Aug 2009, Chris Fields wrote:

> (BTW, this is re: the reimplementation of major chunks of BioPerl using 
> Moose, Biome: http://github.com/cjfields/biome/tree/)
>
> Locations should use a Role (specifically, Biome::Role::Range), so  
> start/end/strand should be attributes, not methods.  With attributes the 
> best way to do this is probably with a builder, and lazily (start  
> requires end, and vice versa).  Factor out the common code as Tomas  
> indicates.  BTW, the $self->throw() is akin to BioPerl's $self->throw() 
> exception handling; it simply catches any exceptions and passes them to 
> the metaclass exception handling.
>
> I've been thinking about making the Range role abstract for this very  
> reason (or defining very basic attributes); something like:
>
> ----------------------------
>
> package Bio::Role::Range;
>
> requires qw(_build_start _build_end _build_strand);
>
> # also require other methods which need to be defined in implementation
>
> has 'start' => (
>      isa      => 'Int',
>      is       => 'rw',
>      builder  => '_build_start',
>      lazy     => 1
> );
>
> # same for end, strand (except strand has a different isa via  
> MooseX::Types)
> ....
>
> package Bio::Location::Foo;
>
> with 'Bio::Role::Range';
>
> sub _build_start {
>    # for location-specific start
> }
>
> sub _build_end {
>    # for location-specific end
> }
>
> sub _build_strand {
>    # for location-specific strand
> }
>
> sub _common_build_method {
>    # factor out common code here, call from other builders
> }
>
> ----------------------------

This plan makes things much clearer. Currently the BioMe::Role::Location has a 'requires' keyword and rest of the 
location modules consume that role to have its own implementation. At
this point on BioMe::Location::Atomic has attribute based 'start' and
'end' implememtation. I got a bit confused because in current bioperl
'Bio::Location::Simple' inherits from 'Bio::Location::Atomic' and when
i am trying to follow that path in BioMe it has to override that method.
So, my question is do all the location modules really needs to inherits
from each other. I am totally aware about the origianl design ideas but
it would be better to have a flatten hierarchy if possible. 
One more thing,  what about putting the 'start',  'end'  and the other
common base attributes in BioMe::Role::Location instead of
BioMe::Role::Range. I am not sure which would be correct from bioperl
stand of view,  just throwing out an idea.  


>
> Also, I think the Coordinate-related stuff should be simplified down to a 
> trait or an attribute; they bring in way too much overhead in bioperl w/o 
> much added value.

You mean instead of having 'builder' method,  having a specialized
traits handling those. That sounds like even better.  

-siddhartha


>
> And now back to your regular Moose-related broadcast...
>
> chris
>
> On Aug 11, 2009, at 9:27 PM, Siddhartha Basu wrote:
>
> > Hi,
> > In one my classes i have this boilerplate code block that is repeated 
> > all
> > over ....
> >
> > sub start {
> >    my ( $self,  $value ) = @_;
> >    $self->{'_start'} = $value if defined $value;
> >
> > ## -- from here
> >    $self->throw( "Only adjacent residues when location type "
> >          . "is IN-BETWEEN. Not ["
> >          . $self->{'_start'}
> >          . "] and ["
> >          . $self->{'_end'}
> >          . "]" )
> >      if defined $self->{'_start'}
> >      && defined $self->{'_end'}
> >      && $self->location_type eq 'IN-BETWEEN'
> >      && ( $self->{'_end'} - 1 != $self->{'_start'} );
> >    return $self->{'_start'};
> > ## -- here
> >
> > }
> >
> > then again ....
> >
> > sub end {
> >    my ( $self,  $value ) = @_;
> >
> >    $self->{'_end'} = $value if defined $value;
> >
> >    #assume end is the same as start if not defined
> >    if ( !defined $self->{'_end'} ) {
> >        if ( !defined $self->{'_start'} ) {
> >            $self->warn('Calling end without a defined start  
> > position');
> >            return;
> >        }
> >        $self->warn('Setting start equal to end');
> >        $self->{'_end'} = $self->{'_start'};
> >    }
> >
> > ## ----
> >
> >    $self->throw( "Only adjacent residues when location type "
> >          . "is IN-BETWEEN. Not ["
> >          . $self->{'_start'}
> >          . "] and ["
> >          . $self->{'_end'}
> >          . "]" )
> >      if defined $self->{'_start'}
> >      && defined $self->{'_end'}
> >      && $self->location_type eq 'IN-BETWEEN'
> >      && ( $self->{'_end'} - 1 != $self->{'_start'} );
> >
> >    return $self->{'_end'};
> > #---------
> > }
> >
> >
> > Is there any way moose can be used here for more code resuage. I  
> > thought
> > about converted it to a type but still couldn't figure out how that  
> > can
> > be done.
> >
> >
> > thanks,
> > -siddhartha
>