Hello all.
I'm having trouble with the FASTA Parser presented in BioJava in Anger.
I just don't seem to be able to get any results from my file. Here is
the script:
import java.io.*;
import java.util.*;
import org.biojava.bio.program.sax.*;
import org.biojava.bio.program.ssbind.*;
import org.biojava.bio.search.*;
import org.biojava.bio.seq.db.*;
import org.xml.sax.*;
import org.biojava.bio.*;
public class BlastParser {
/**
* String location is the full path of a FASTA output file
*/
public static void main(String[] args) {
try {
//get the Blast input as a Stream
String location = "Full//path//of//file";
InputStream is = new FileInputStream(location);
//make a FastaSearchSAXParser
FastaSearchSAXParser parser = new FastaSearchSAXParser();
//make the SAX event adapter that will pass events to a Handler.
SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
//set the parsers SAX event adapter
parser.setContentHandler(adapter);
//The list to hold the SeqSimilaritySearchResults
List results = new ArrayList();
//create the SearchContentHandler that will build
SeqSimilaritySearchResults
//in the results List
SearchContentHandler builder = new BlastLikeSearchBuilder(results,
new DummySequenceDB("queries"), new
DummySequenceDBInstallation());
//register builder with adapter
adapter.setSearchContentHandler(builder);
//parse the file, after this the result List will be populated with
//SeqSimilaritySearchResults
parser.parse(new InputSource(is));
//output some blast details
for (Iterator i = results.iterator(); i.hasNext(); ) {
SeqSimilaritySearchResult result =
(SeqSimilaritySearchResult)i.next();
Annotation anno = result.getAnnotation();
for (Iterator j = anno.keys().iterator(); j.hasNext(); ) {
Object key = j.next();
Object property = anno.getProperty(key);
System.out.println(key+" : "+property);
}
System.out.println("Hits: ");
//list the hits
for (Iterator k = result.getHits().iterator(); k.hasNext(); ) {
SeqSimilaritySearchHit hit =
(SeqSimilaritySearchHit)k.next();
System.out.print("\tmatch: "+hit.getSubjectID());
System.out.println("\te score: "+hit.getEValue());
}
System.out.println("\n");
}
}
catch (SAXException ex) {
//XML problem
ex.printStackTrace();
}catch (IOException ex) {
//IO problem, possibly file not found
ex.printStackTrace();
}
}
}
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