[Biojava-dev] porting HMM classes from bj1.8 to bj3

[Andreas Prlic]

Hi Zhihua,

good to see that your message made it through in the end. What IDE are
you using? I recommend checking out the latest version of
biojava-legacy (1.8) and  doing the refactoring on the (legacy) core
module. A first step could be to break out a HMM module out of the old
core. Then this module could be migrated to the 3.X design.  I see
some difficulty coming up with how to deal with the Symbols from the
1.X world, so let's keep discussing this as you make progress...

Andreas

On Fri, Aug 12, 2011 at 7:54 AM, Scooter Willis <HWillis at scripps.edu> wrote:
> I think first step is to take the HMM classes from 1.8 and migrate with
> zero dependencies of any non HMM classes in Biojava 1.8. If you can it to
> compile with a minimal number of external packages then migration as a
> standalone module should be easy. If you work with Strings as inputs that
> should help minimize dependencies.
>
> On 8/12/11 10:45 AM, "zhihuali" <lzhtom at hotmail.com> wrote:
>
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>>Dear all,
>>
>>I have been trying to post this message several times now but couldn't
>>see it in the list. Hopefully this time it will get through. If you
>>received
>>multiple copies of this email please forgive me.
>>
>>I was pointed to here by Andreas and Sylvain from LinkedIn.
>>Basically we felt that a great missing piece in bj3 from legacy biojava
>>is HMM classes. And I'd like to take on this task. Maybe the first
>>thing is to migrate bj1.8's dp package and related packages to bj3.
>>Could anyone give me directions to get it started?
>>
>>Thanks a lot!
>>
>>Zhihua Li
>
>
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