[Bioperl-l] For CVS developers - throw_not_implemented

[Hilmar Lapp]

This is documentation cruft resulting from copy&paste w/o later  
fixing it. (which isn't a justification)

Note that not implementing the write is as legitimate as not  
implementing the read method ... It should be pointed out in the  
documentation though that it will depend on the actual implementation  
of the format whether it supports reading or writing or both.

	-hilmar

On May 31, 2006, at 5:40 PM, Chris Fields wrote:

> I think, as long as it's reflected in the docs that something  
> doesn't work
> (hasn't been implemented) then there's no problem.  It's when the  
> docs are
> misleading that we run into problems.
>
> The sticking point lies with some classes, such as IO classes (like  
> SeqIO,
> or Restrict::IO, with read and write methods) where the IO base class
> specifies that it is possible to read and write a particular format  
> but the
> actual implementation varies according to whether or not the  
> derived class
> overrides the base or interface method (in other words, 'doesn't  
> work as
> advertised' only in specific circumstances).  I don't know how to  
> solve this
> issue except to add in the docs that specific formats don't implement
> write() methods.
>
> Personally, I haven't had an issue with it and it probably makes no
> difference, but I think it needs to be pointed out.  The most  
> extreme I ran
> into was Bio::Restriction::IO, which had 3 out of 4 plugin modules  
> that
> didn't implement the write() method but left this in the synopsis  
> in POD:
>
>     use Bio::Restriction::IO;
>
>     $in  = Bio::Restriction::IO->new(-file => "inputfilename" ,
>                                      -format => 'withrefm');
>     $out = Bio::Restriction::IO->new(-file => ">outputfilename" ,
>                                      -format => 'bairoch');
>     my $res = $in->read; # a Bio::Restriction::EnzymeCollection
>     $out->write($res);
>
>   # or
>
>   #    use Bio::Restriction::IO;
>   #
>   #    #input file format can be read from the file extension (dat| 
> xml)
>   #    $in  = Bio::Restriction::IO->newFh(-file => "inputfilename");
>   #    $out = Bio::Restriction::IO->newFh('-format' => 'xml');
>   #
>   #    # World's shortest flat<->xml format converter:
>   #    print $out $_ while <$in>;
>
> None of this code works; in fact, no XML parser even exists for  
> these IO
> classes!  Bio::AlignIO also has a few as well (maf and Stockholm  
> formats
> don't write).
>
> Chris
>
>
>> -----Original Message-----
>> From: Hilmar Lapp [mailto:hlapp at gmx.net]
>> Sent: Wednesday, May 31, 2006 4:22 PM
>> To: Chris Fields
>> Cc: lstein at cshl.edu; bioperl-l at lists.open-bio.org; 'Heikki  
>> Lehvaslaiho'
>> Subject: Re: [Bioperl-l] For CVS developers - throw_not_implemented
>>
>>
>> On May 31, 2006, at 4:40 PM, Chris Fields wrote:
>>
>>> What about modules that have 'throw_not_implemented' statements
>>> present?
>>
>> Those are often if not always legitimate - the problem are those that
>> don't have them but fail to override an inherited interface or
>> abstract method.
>>
>> If something is not implemented what is the better way to express
>> this other than throwing an exception? (and if it's not an interface
>> or abstract base class, saying so in the documentation)
>>
>> 	-hilmar
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================