[Biojava-l] fileToBiojava question

[Bernd Jagla]

  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
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>