[Biojava-l] FASTA Parser problems

[Richard HOLLAND]

Could you send me the input file you are using as an attachment
(directly, not via the mailing list as it will get removed), I can then
run the script and compare input to output.

Also, which BioJava version are you using?

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Williamson, TC
> Sent: Friday, July 08, 2005 10:29 PM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] FASTA Parser problems
> 
> 
> 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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