[Biojava-l] why can't biojava fold RNA?

[Mark Fortner]

You might try JNA instead of JNI. It's easier to use.  However, I'd be
reticent about calling it frequently in a loop, as there is some overhead
involved.

Mark


On Tue, Sep 20, 2011 at 6:14 PM, Daniel Quest <daniel.quest at gmail.com>wrote:

> I don't quite think this answers the question.
>
> If you want to execute c/c++/fortran/legacy code from java, you can do a
> system exec from within java.  Or you can play around with jni but my
> experiences with that have not been good
>
> Does biojava have the ability to execute a stand alone program?  If not I
> have some code lying around you guys can have
>
> Daniel
>
> Sent from my iPod
>
> On Sep 20, 2011, at 11:11 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
> > If all your code is in Java and you have binaries for some external
> > software you can easily wrap it from Java and trigger the execution.
> >
> > Andreas
> >
> > On Tue, Sep 20, 2011 at 2:09 AM, quan zou <guoer713108 at gmail.com> wrote:
> >> Thanks, however, there is no java code. it cannot be imported into my
> java
> >> project.
> >>
> >> 2011/9/20 Andreas Prlic <andreas at sdsc.edu>
> >>>
> >>> Hi Quan,
> >>>
> >>> the Vienna RNA package is available as open source.  Did you take a
> look
> >>> at it?
> >>>
> >>> Andreas
> >>>
> >>>
> >>> On Mon, Sep 19, 2011 at 9:18 PM, quan zou <guoer713108 at gmail.com>
> wrote:
> >>>> Dear all,
> >>>>
> >>>>        Is there any java program or jar which can fold a RNA sequence
> to
> >>>> a
> >>>> secondary structure? Such as RNAfold?
> >>>>
> >>>>       Why RNAfold/ Vienna Package have not been contained in Biojava?
> >>>>
> >>>>                 Quan
> >>>> _______________________________________________
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> >>>>
> >>
> >>
> >
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