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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