[Biojava-l] fileToBiojava question

[Bernd Jagla]

  Bingo, I got it.
The problem was that I wasn't using ant to build the library but rather 
relied on Eclipse to do the job...
now it seems to be working.
Actually when including bytecode.jar as Richard suggested it even works 
with my KNIME applicattion...

Sorry for that...

But maybe the iterator would be good to include in the next release???

Cheers,

Bernd

On 9/23/2010 4:53 PM, Bernd Jagla wrote:
>  Just to make sure that the "small" modification is not the issue:
>
> I added the follwing in FastqReader.java
>    Iterable<Fastq> read(InputStream inputStream) throws IOException;
>
>     Fastq readNext(InputStream inputStream) throws IOException;
>
> Since I needed an iterator for a different project.
>
> Best,
>
> Bernd
>
>
>
> On 9/23/2010 4:40 PM, Bernd Jagla wrote:
>>  Hello again,...
>>
>> I am still struggling with my little problem. I am getting closer I 
>> think...
>> I made some minor modifications to some biojava files and would like 
>> to compile it under 1.6. Is this possible?
>>
>> When I compare version 1.7.1 with mine the only difference seems to 
>> be the java version. And the sample code runs with your but not with 
>> mine... ;(
>>
>> I get the following error message:
>>
>> Exception in thread "main" java.lang.NoClassDefFoundError: 
>> org/biojava/utils/bytecode/CodeException
>>     at 
>> org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1273)
>>     at 
>> org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1817)
>>     at 
>> org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:54)
>>     at 
>> org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(RichFeature.java:167)
>>     at 
>> org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java:61)
>>     at 
>> org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(SimpleRichSequenceBuilder.java:100)
>>     at 
>> org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(SimpleRichSequenceBuilder.java:81)
>>     at 
>> org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder(SimpleRichSequenceBuilderFactory.java:68)
>>     at 
>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
>>     at org.pasteur.pf2.biojava.biojavaIO.execute(biojavaIO.java:54)
>>     at org.pasteur.pf2.biojava.biojavaIO.main(biojavaIO.java:29)
>> Caused by: java.lang.ClassNotFoundException: 
>> org.biojava.utils.bytecode.CodeException
>>     at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
>>     at java.security.AccessController.doPrivileged(Native Method)
>>     at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>>     at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>>     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>>     at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
>>     at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
>>     ... 11 more
>>
>>
>> Do you think this problem can be due to the compiler???
>>
>> Reading through some of the information on the web about 
>> NoClassDefFoundError it should be something like or my class path is 
>> messed or something like that...
>>
>> Thanks for any tip/hint and how to identify and solve this problem
>>
>> Best,
>>
>> Bernd
>>
>> _______________________________________________
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>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>
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