Hi,
I wrote a fasta parser for biology computing
http://pastebin.geany.org/yheQN/

I would like to get your experience to know if the writer could be better. The given parser use MmFile and Phobos range.

fasta specification format => http://en.wikipedia.org/wiki/FASTA_format

Le dimanche 11 novembre 2012 à 18:34 +0100, bioinfornatics a écrit :
> Hi,
> I wrote a fasta parser for biology computing
> http://pastebin.geany.org/yheQN/
> 
> I would like to get your experience to know if the writer could be better. The given parser use MmFile and Phobos range.
> 
> fasta specification format => http://en.wikipedia.org/wiki/FASTA_format
> 

minor update http://pastebin.geany.org/OgUHg/ is now a forwardRange

On 2012-34-11 18:11, bioinfornatics <bioinfornatics@fedoraproject.org> wrote:

> Hi,
> I wrote a fasta parser for biology computing
> http://pastebin.geany.org/yheQN/
>
> I would like to get your experience to know if the writer could be
> better. The given parser use MmFile and Phobos range.
>
> fasta specification format => http://en.wikipedia.org/wiki/FASTA_format

Not available (anymore). That's a bummer.

Also, obligatory 'Red unz go fasta!'

-- 
Simen

Le dimanche 11 novembre 2012 à 19:58 +0100, Simen Kjaeraas a écrit :
> On 2012-34-11 18:11, bioinfornatics <bioinfornatics@fedoraproject.org> wrote:
> 
> > Hi,
> > I wrote a fasta parser for biology computing
> > http://pastebin.geany.org/yheQN/
> >
> > I would like to get your experience to know if the writer could be better. The given parser use MmFile and Phobos range.
> >
> > fasta specification format => http://en.wikipedia.org/wiki/FASTA_format
> 
> Not available (anymore). That's a bummer.
> 
> Also, obligatory 'Red unz go fasta!'
> 

oops sorry http://dpaste.dzfl.pl/dae66c94

Le dimanche 11 novembre 2012 à 18:34 +0100, bioinfornatics a écrit :
> Hi,
> I wrote a fasta parser for biology computing
> http://pastebin.geany.org/yheQN/
> 
> I would like to get your experience to know if the writer could be better. The given parser use MmFile and Phobos range.
> 
> fasta specification format => http://en.wikipedia.org/wiki/FASTA_format
> 

Here i continue to enhance the parser i fail about reverse range: http://dpaste.dzfl.pl/1f0aef89

i need to initialize the range:
- popFront if we go forward
- popBack if we go back

how can i detect this instead to use the boolean isForward?

On 11/11/2012 03:55 PM, bioinfornatics wrote:
> Le dimanche 11 novembre 2012 à 18:34 +0100, bioinfornatics a écrit :
>> Hi,
>> I wrote a fasta parser for biology computing
>> http://pastebin.geany.org/yheQN/
>>
>> I would like to get your experience to know if the writer could be
>> better. The given parser use MmFile and Phobos range.
>>
>> fasta specification format =>  http://en.wikipedia.org/wiki/FASTA_format
>>
>
> Here i continue to enhance the parser i fail about reverse range:
> http://dpaste.dzfl.pl/1f0aef89
>
> i need to initialize the range:
> - popFront if we go forward
> - popBack if we go back
>
> how can i detect this instead to use the boolean isForward?
>

If a range provides back() and popBack() in addition to front() and popFront() then it looks like a BidirectionalRange. The users would expect to use a byFasta struct as a BidirectionalRange.

However, both front() and back() use the same member, _fasta, meaning that the front and back of the range are the same.

I am not familiar with the Fasta format but if it is not by nature bidirectional, I think you shouldn't provide back() and popBack().

Ali

11/11/2012 9:34 PM, bioinfornatics пишет:
> Hi,
> I wrote a fasta parser for biology computing
> http://pastebin.geany.org/yheQN/
>
> I would like to get your experience to know if the writer could be
> better. The given parser use MmFile and Phobos range.
>
> fasta specification format => http://en.wikipedia.org/wiki/FASTA_format
>

I'd like to spread the word of the proper toString signature that doesn't need appender.

void toString(scope delegate(const(char)[]) sink) const{
 //same code, but replace fasta.put(x) with sink(x)
}



-- 
Dmitry Olshansky

On Monday, 12 November 2012 at 09:16:54 UTC, Dmitry Olshansky wrote:
> 11/11/2012 9:34 PM, bioinfornatics пишет:
>> Hi,
>> I wrote a fasta parser for biology computing
>> http://pastebin.geany.org/yheQN/
>>
>> I would like to get your experience to know if the writer could be
>> better. The given parser use MmFile and Phobos range.
>>
>> fasta specification format => http://en.wikipedia.org/wiki/FASTA_format
>>
>
> I'd like to spread the word of the proper toString signature that doesn't need appender.
>
> void toString(scope delegate(const(char)[]) sink) const{
>  //same code, but replace fasta.put(x) with sink(x)
> }

Is there any documentation for this signature?

11/12/2012 2:14 PM, Tobias Pankrath пишет:
> On Monday, 12 November 2012 at 09:16:54 UTC, Dmitry Olshansky wrote:
>> 11/11/2012 9:34 PM, bioinfornatics пишет:
>>> Hi,
>>> I wrote a fasta parser for biology computing
>>> http://pastebin.geany.org/yheQN/
>>>
>>> I would like to get your experience to know if the writer could be
>>> better. The given parser use MmFile and Phobos range.
>>>
>>> fasta specification format => http://en.wikipedia.org/wiki/FASTA_format
>>>
>>
>> I'd like to spread the word of the proper toString signature that
>> doesn't need appender.
>>
>> void toString(scope delegate(const(char)[]) sink) const{
>>  //same code, but replace fasta.put(x) with sink(x)
>> }
>
> Is there any documentation for this signature?

Now that could be why nobody uses it :)

This hole in documentation must be filled because it is a solution to allocation happiness of toString. AFAIK it supposed to be the new way of string conversion and the old one eventually deprecated.

-- 
Dmitry Olshansky

Le dimanche 11 novembre 2012 à 18:34 +0100, bioinfornatics a écrit :
> Hi,
> I wrote a fasta parser for biology computing
> http://pastebin.geany.org/yheQN/
> 
> I would like to get your experience to know if the writer could be better. The given parser use MmFile and Phobos range.
> 
> fasta specification format => http://en.wikipedia.org/wiki/FASTA_format
> 

Tanks to all this one http://dpaste.dzfl.pl/1f0aef89 works has
bidirectional range :-)
I will take a look to Dmitry comment about toString.
at Ali about fasta, fasta format is as an array where is wrote into a
plain text file. So they are no restriction in more it is not more
harder to parse it from forward or reverse with mmfile i do not know how
do same this regular file struct.