[Biojava-l] Reflection Errors reading FASTA file using Biojava.

[Richard Holland]

The exception stack shows that the error is being thrown by some part of
the software package called com.opensymphony.xwork2.

This is not part of BioJava.

If you try running your code outside of the Tomcat/Struts environment, I
think you'll find it works fine (it does for me, anyhow!).

I suspect that you have some kind of profiling tool active which is
interfering with the process. Try disabling profiling and try again.

If this persists, you should attempt to contact the manufacturers of your
profiling tool (which I guess is OpenSymphony, based on the classnames
involved) to see if they can tell you what would cause their software to
throw such exceptions. If they can trace it to a particular fault in
BioJava then we would be glad to hear of it, but we are unable to do this
tracing ourselves as the exception is not being thrown from within
BioJava.

cheers,
Richard

On Fri, September 21, 2007 5:08 pm, Svancara, Randall wrote:
> Hi,  I am new to biojava.  I am trying to read a fasta file using the
> following code:
>
> 1. public Fasta(File fastafile) throws Exception{
> 2.  this.fastafile = fastafile;
> 3.  BufferedReader br = new BufferedReader(new FileReader(fastafile));
>
> 4.  FastaFormat fastaformat = new FastaFormat();
> 5.  if(fastaformat.canRead(fastafile)){
> 6.    SymbolTokenization cTok =
> fastaformat.guessSymbolTokenization(fastafile);
>
> 7.    RichSequenceIterator it = RichSequence.IOTools.readFasta(br,cTok,
> RichObjectFactory.getDefaultNamespace());
>
> 8.    while(it.hasNext()){
> 9.      Sequence seq = it.nextRichSequence();
> 10.    }
> 11.  }
> 13. }
>
> My problem is that I want to be able to read a fasta file and figure out
> first if it is a protein or DNA sequence file, and next parse out the
> sequences.  However, when I run this code i receive the following
> errors.  I have only included part of the exception stack.  However, you
> can see that there are reflection errors being thrown.  I am using
> biojava in a struts2 environment running on apache tomcat 6.0.12 with
> JDK 1.6 release 2.
>
> javax.servlet.ServletException:
> java.lang.reflect.InvocationTargetException
> 	org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:515)
> 	org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:419)
>
> root cause
>
> java.lang.reflect.InvocationTargetException
> 	sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> 	sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> 	java.lang.reflect.Method.invoke(Method.java:597)
> 	com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:404)
> 	com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:267)
> 	com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:229)
> 	com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:123)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
> 	com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
> 	com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
> 	com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:167)
> 	com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
> 	com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
> 	com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
> 	org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:83)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
> 	com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
> 	com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
> 	com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:121)
> 	com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:86)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
> 	com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile(UtilTimerStack.java:455)
> 	com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:221)
> 	org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:170)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:224)
> 	com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling(DefaultActionInvocation.java:223)
>
>
> Thanks,
>
> --
> Randall Svancara
> System Administrator
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK