Re: [Biojava-l] blast parsing

Simon Foote Wed, 19 Mar 2003 10:16:08 -0800

The root cause:

java.lang.NoClassDefFoundError:
org/biojava/bio/program/sax/BlastLikeSAXParser

seems to indicate that the biojava.jar is not available to your webapp. Make sure its in the WEB-INF/lib directory of your webapp.

Cheers,
Simon

dkabic01 wrote:

hi I am new to biojava having some difficulty parsing my output. I am using HT-BLast which is for SGI computer systems . I am calling HT-BLAST program from my servlet program and it working fine. Problem arise when i add code for parsing the output. given below is the code for parsing the output and error
message displayed my the TOMCAT server when servlet is executed.
code is :
InputStream is = new
FileInputStream("/vol1/people/dinesh/htblast/test.out");
  try {
  XMLReader parser = (XMLReader) new BlastLikeSAXParser();
  ((BlastLikeSAXParser)parser).setModeLazy();
  SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
  parser.setContentHandler(adapter);
  List results = new ArrayList();
  SearchContentHandler builder = new BlastLikeSearchBuilder(results);
  adapter.setSearchContentHandler(builder);
  parser.parse(new InputSource(is));
  for (Iterator i = results.iterator(); i.hasNext(); ) {
  SeqSimilaritySearchResult result = (SeqSimilaritySearchResult)i.next();
  for (Iterator i2 = result.getHits().iterator(); i2.hasNext(); ) {
  SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)i2.next();
  out.println("sequence:\t"+hit.getSequenceID());
  out.println(" bits:\t"+hit.getScore());
  out.println(" e:\t"+hit.getEValue());
  }
  }
 }catch (SAXException ex) {
  ex.printStackTrace();
   }
and error messages is:

type Exception report

message Internal Server Error

description The server encountered an internal error (Internal Server Error)

that prevented it from fulfilling this request.

exception

javax.servlet.ServletException: Servlet execution threw an exception at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application Fi lterChain.java:269, Compiled Code) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ai n.java:193, Compiled Code) at filters.ExampleFilter.doFilter(ExampleFilter.java:149, Compiled Code) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application Fi lterChain.java:213, Compiled Code) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ai n.java:193, Compiled Code) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.ja va :243, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.ja va :190, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase .j ava:475, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2347, Compiled Code) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve. ja va:170, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:170 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:468, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java :1 74, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.connector.http.HttpProcessor.process(HttpProcessor.java: 10 27, Compiled Code) at org.apache.catalina.connector.http.HttpProcessor.run(HttpProcessor.java:1125 , Compiled Code) at java.lang.Thread.run(Thread.java:484, Compiled Code)

root cause

java.lang.NoClassDefFoundError: org/biojava/bio/program/sax/BlastLikeSAXParser at FormProcessingServlet.doPost(FormProcessingServlet.java:81, Compiled Code) at javax.servlet.http.HttpServlet.service(HttpServlet.java:760, Compiled Code) at javax.servlet.http.HttpServlet.service(HttpServlet.java:853, Compiled Code) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application Fi lterChain.java:247, Compiled Code) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ai n.java:193, Compiled Code) at filters.ExampleFilter.doFilter(ExampleFilter.java:149, Compiled Code) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application Fi lterChain.java:213, Compiled Code) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ai n.java:193, Compiled Code) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.ja va :243, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.ja va :190, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase .j ava:475, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2347, Compiled Code) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve. ja va:170, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:170 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:468, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 64 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java :1 74, Compiled Code) at org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:5 66 , Compiled Code) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472, Compiled Code) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943, Compiled Code) at org.apache.catalina.connector.http.HttpProcessor.process(HttpProcessor.java: 10 27, Compiled Code) at org.apache.catalina.connector.http.HttpProcessor.run(HttpProcessor.java:1125 , Compiled Code) at java.lang.Thread.run(Thread.java:484, Compiled Code)

please advice.

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Re: [Biojava-l] blast parsing

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