[Biojava-l] Usual newbie mistake ?

[Thomas Down]

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On Wed, Jan 16, 2002 at 07:00:44PM +0100, Michal Kurowski wrote:
> Hi,
> According to some previous posts it seems I've got an usual beginner
> mistake in here. When I type "javac seq/TestEmbl.java" I got:
> 
> seq/TestEmbl.java:23: cannot resolve symbol
> symbol  : class SymbolParser
> location: class seq.TestEmbl
>       SymbolParser rParser = alpha.getParser("token");
>       ^
> seq/TestEmbl.java:23: cannot resolve symbol
> symbol  : method getParser  (java.lang.String)
> location: interface org.biojava.bio.symbol.Alphabet
>       SymbolParser rParser = alpha.getParser("token");


No, it's a usual developer (me, in this case) not-checking-that-
things-compile mistake -- sorry!

I've attached a corrected version.  The only changes are:

  SymbolParser -> SymbolTokenization
  getParser(String name) -> getTokenization(String name);

This is the correct API for the forthcoming 1.2 release
series.

Hope this helps,

    Thomas.


PS.  Note that these demos are all a bit old.  Most people would
     actually use the convenient method:

         SeqIOTools.readEmbl();

     You might like to look at TestEmbl2.java to see how this
     is used.

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package seq;

import java.io.*;

import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;

public class TestEmbl {
  public static void main(String [] args) {
    try {
      if(args.length != 1) {
        throw new Exception("Use: TestEmbl emblFile");
      }
      
      File emblFile = new File(args[0]);
      SequenceFormat eFormat = new EmblLikeFormat();
      BufferedReader eReader = new BufferedReader(
        new InputStreamReader(new FileInputStream(emblFile)));
      SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY);
      Alphabet alpha = DNATools.getDNA();
      SymbolTokenization rParser = alpha.getTokenization("token");
      SequenceIterator seqI =
        new StreamReader(eReader, eFormat, rParser, sFact);
        
      while(seqI.hasNext()) {
        Sequence seq = seqI.nextSequence();
        System.out.println(seq.getName() + " has " + seq.countFeatures() + " features");
        eFormat.writeSequence(seq, System.out);
        System.out.println("pigs");
      }
    } catch (Throwable t) {
      t.printStackTrace();
      System.exit(1);
    }
  }
}

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