[Biojava-l] blast parsing

[Simon Foote]

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.
>
>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>  
>