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

[Svancara, Randall]

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