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

[Andreas Prlic]

A simple way to run an external program is via ProcessBuilder (since Java 1.5)

http://download.oracle.com/javase/1.5.0/docs/api/java/lang/ProcessBuilder.html

Andreas


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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>