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

Sat Sep 22 11:07:56 UTC 2007

>From a quick look at the stack trace it seems it is Struts 2.0 that is
doing the reflection (and failing).

I don't see any indication that this is a biojava problem. From the
trace it doesn't look like any biojava methods have been called.

- Mark

On 9/22/07, Randall Svancara <rsvancara at wsu.edu> wrote:
> I have created a stand alone class that calls this same code as
> described below and and it executes just fine by itself.  However using
> Struts 2.0 that uses classes from WebWork MVC framework, this same code
> fails.  If i comment out lines 8,9,10, there are no errors.  So does the
> iterator use reflection to obtain at run-time the correct sequence
> object to load?
>
> Randall
>
> On Fri, 2007-09-21 at 18:59 +0100, Richard Holland wrote:
> > 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
> > >
> >
> >
> --
> Randall Svancara
> System Administrator
> Horticulture and Landscape Architecture
> 509-335-7093
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