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On 27/01/12 20:22, Wicks, Benjamin wrote:
> Nico,
>
> Now I am trying to work with the jar that was created. I am finding
> that there must be a file that is missing. Eclipse is giving me a
> compilation error: "The type org.sbml.jsbml.ext.AbstractSBasePlugin
> cannot be resolved. It is indirectly referenced from required .class
> files". When I look through the folder
> extensions/qual/src/org/sbml/jsbml/ext, there is no
> AbstractSBasePlugin class though that is where the import in the
> QualitativeModel class tells it to look.
>
> Do I need to download additional to make this work?

Now, to be able to work with the jar files, you need the newly created
jsbml jar file that is on the build folder + all the dependency jars
that are on the
lib folder + the sbml-qual jar.

I you were using the jsbml jar file with dependencies, you could
generate a new one with the command :

ant bigjar

Then, if you include this jar + the sbml-qual jar, it should work as well.

The AbstractSBasePlugin is included in the standard jsbml jar as it is
not specific to one package.

Cheers,
Nico

>
> On Fri, Jan 27, 2012 at 1:27 PM, Wicks, Benjamin <bwicks@unomaha.edu
> <mailto:bwicks@unomaha.edu>> wrote:
>
> Thanks again. That worked very well.
>
>
> On Tue, Jan 24, 2012 at 2:42 PM, Nicolas Rodriguez
> <rodrigue@ebi.ac.uk <mailto:rodrigue@ebi.ac.uk>> wrote:
>
> Hi Ben,
>
> This is my mistake, you need to compile the main jsbml jar
> files first.
>
> after doing the checkout (svn co
> https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk jsbml)
> go to the root of the checkout :
> cd jsbml
> ant jar
>
> That will generate the jsbml jar file. Now, when you go to the
> qual folder the compilation should be fine.
>
> Nico
>
> Le 24/01/2012 18:43, Wicks, Benjamin a écrit :
>
> Hello all,
>
> I am working on a project that I would like to use the
> jsbml-qual library
> for. I received instructions on how to set up the code
> from the jsbml
> repository via the sbml-qual mailing list. I am looking
> for some further
> help here because I got a BUILD FAILED error when I tried
> to run:
>
> cd extensions/qual
> ant jar
>
> Here are the last few lines of the output from that command:
>
> [javac] Transition.java:273: cannot find symbol
> [javac] symbol : class ListOf
> [javac] location: class org.sbml.jsbml.ext.qual.Transition
> [javac] public ListOf<Output> getListOfOutputs() {
> [javac] ^
> [javac] 100 errors
>
> BUILD FAILED
> /home/ben/jsbml/extensions/qual/build.xml:183: Compile
> failed; see the
> compiler error output for details.
>
> Total time: 1 second
>
> --
> I could not locate the compiler error output for details.
> What should I do
> differently?
>
> Thank you,
> Ben
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>
>
>
>
> --
> Benjamin Wicks
> Bioinformatics Student
> University of Nebraska at Omaha 2014
> bwicks@unomaha.edu <mailto:bwicks@unomaha.edu>
> 402.301.7127 <tel:402.301.7127>
>
>
>
>
> --
> Benjamin Wicks
> Bioinformatics Student
> University of Nebraska at Omaha 2014
> bwicks@unomaha.edu <mailto:bwicks@unomaha.edu>
> 402.301.7127
>

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