[Biojava-dev] Problems building biojava v2 (trunk or alpha1)

[Matthew Pocock]

Hi Bruno,

Great to hear that you are interested. Sorry for the problems some of 
you have had compiling the code - I didn't realise how in-flux the beta 
sdk was, or I would have waited untill the next official beta release of 
the sdk.

It would be realy helpfull at this point to get a list from people about 
what sucks in biojava at the moment - glaringly missing functionality or 
realy confusing API or anything else for that matter. So far, none of 
the biology APIs are set in stone for bjv2.

For those of you who can't test out Medusa, here is a program that 
parses any text file into tag-value events, and below is a program that 
loads in a sequence file and prints out some vital stats, just so you 
can get a feel for the syntax.

------

import org.bjv2.io.FormatReader;
import org.bjv2.io.IOListeners;
import org.bjv2.io.IOListener;
import org.bjv2.io.FormatFactories;

import java.io.File;

/**
 * @author Matthew Pocock
 */
public class ReadGuessedFormatCompact
{
  public static void main(String[] args)
          throws Throwable
  {
    File inFile = new File(args[0]);
    FormatReader reader = FormatFactories.findReader(inFile);
    IOListener listener = IOListeners.echo(System.out, 2);
    for (reader.read(listener); reader.hasNext(); reader.read(listener)) {
      // don't do anything here - the events are being processed by listener
    }
  }
}

----

import org.bjv2.seq.Sequence;
import org.bjv2.seq.Sequences;
import org.bjv2.seq.Feature;
import org.bjv2.integrator.Integrated;
import org.bjv2.integrator.Integrator;

import java.io.File;

/**
 * @author Matthew Pocock
 */
public class LoadSequence
{
  public static void main(String[] args)
          throws Throwable
  {
    File seqFile = new File(args[0]);
    for(Sequence seq: Sequences.load(seqFile)) {
      System.out.println("Sequence: " + seq.getIdentifier());
      System.out.println("Length: " + seq.getSymbolList().length());
      System.out.println("Features: " + seq.getFeatures().size());
    }
  }
}