[Biojava-l] (no subject)

[Michael L. Heuer]

Thomas,

I'm getting a strange error when serving reference sequence from an
EmblDataSource via the /das/[dsn]/dna request.  No matter what the dna
query ( dna?segment=ACC, dna?segment=ACC:1,100, ...) I receive the same
index out of range exception.  Is this value significant for any reason?

The entry_points request returns an accurate list, leading me to believe
the sequences were loaded from the embl file correctly.

I'm using cvs versions of xdas and biojava.

   michael

---


2002-01-09 16:32:34 - /das: DazzleServerMain: Error writing DNA document -
java.lang.IndexOutOfBoundsException: Index out of range: -1392881928
	at
org.biojava.bio.seq.io.SubArraySymbolList.symbolAt(SubArraySymbolList.java:77)
	at
org.biojava.bio.symbol.AbstractSymbolList$SubList.getAlphabet(AbstractSymbolList.java:169)
	at
org.biojava.bio.symbol.AbstractSymbolList$SubList.seqString(AbstractSymbolList.java:208)
	at
org.biojava.bio.symbol.AbstractSymbolList$SubList.subStr(AbstractSymbolList.java:216)
	at
org.biojava.servlets.dazzle.DazzleServlet.dnaCommand(DazzleServlet.java:680)
	at
org.biojava.servlets.dazzle.DazzleServlet.doGet(DazzleServlet.java:241)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java)
	at org.apache.tomcat.facade.ServletHandler.doService(Unknown
Source)
	at org.apache.tomcat.core.Handler.invoke(Unknown Source)
	at org.apache.tomcat.core.Handler.service(Unknown Source)
	at org.apache.tomcat.facade.ServletHandler.service(Unknown Source)
	at org.apache.tomcat.core.ContextManager.internalService(Unknown
Source)
	at org.apache.tomcat.core.ContextManager.service(Unknown Source)
	at
org.apache.tomcat.modules.server.Http10Interceptor.processConnection(Unknown
Source)
	at org.apache.tomcat.util.net.TcpWorkerThread.runIt(Unknown
Source)
	at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(Unknown
Source)
	at java.lang.Thread.run(Thread.java:484)