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(ApplicationFi
lterChain.java:269, Compiled Code)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChai
n.java:193, Compiled Code)
at filters.ExampleFilter.doFilter(ExampleFilter.java:149, Compiled
Code)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFi
lterChain.java:213, Compiled Code)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChai
n.java:193, Compiled Code)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java
:243, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566
, 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.java
:190, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566
, Compiled Code)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.j
ava:475, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, 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:566
, Compiled Code)
at
org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.ja
va:170, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, Compiled Code)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:170,
Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, Compiled Code)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:468,
Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, 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:566
, 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(ApplicationFi
lterChain.java:247, Compiled Code)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChai
n.java:193, Compiled Code)
at filters.ExampleFilter.doFilter(ExampleFilter.java:149, Compiled
Code)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFi
lterChain.java:213, Compiled Code)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChai
n.java:193, Compiled Code)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java
:243, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566
, 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.java
:190, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566
, Compiled Code)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.j
ava:475, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, 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:566
, Compiled Code)
at
org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.ja
va:170, Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, Compiled Code)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:170,
Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, Compiled Code)
at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:468,
Compiled Code)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564
, 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:566
, 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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