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

[Randall Svancara]

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