[Biojava-dev] ViewSequence

[Warth,Rainer,LAUSANNE,NRC/BAS]

Hi,
	I wanted to try this program from the bioJAVA in ANGER page
(http://www.biojava.org/docs/bj_in_anger/NameChange.htm
). I just pasted the text in the NameChange.java file which is part of the
seq package. My biojava classpath must be okay since I have other classes in
this package, which work fine (e.g. TestEmbl). However, I get the message
that ViewSequence(seq, "ABC123") is not a valid constructor. In addition,
the method writeFasta does not seem to have the right arguments ( line
SeqIOTools.writeFasta(System.out, seq2).
This is confirmed when I try to run it.

java.lang.Error: Unresolved compilation problems: 
	The constructor ViewSequence(Sequence, String) is undefined
	The method writeFasta(OutputStream, SequenceDB) in the type
SeqIOTools is not applicable for the arguments (PrintStream, ViewSequence)

	at seq.NameChange.main(NameChange.java:28)


Does anybody see, what is wrong ?
biojava-1.3.1.jar and bytecode-0.92.jar are on my classpath.


Best, Rainer

--------

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

	public class NameChange {
	  public static void main(String[] args) {
		try {
		  Sequence seq =
	
DNATools.createDNASequence("atgcgctaggctag","gi|12356|ABC123");

		  //create a veiw on the sequence and change its name
		  ViewSequence seq2 = new ViewSequence(seq, "ABC123");

		  //print to FASTA to prove the name has changed
		  SeqIOTools.writeFasta(System.out, seq2);
		}
		catch (IllegalSymbolException ex) {
		  //tried to make seq with non DNA symbol
		  ex.printStackTrace();
		}catch (IOException ex) {
		  //couldn't print seq2 to System out??
		  ex.printStackTrace();
		}
	  }
	}

---
Dr. Rainer Warth
Research Scientist Bioinformatics

BioAnalytical Science Department
Nestlé Research Center
Vers-Chez-LES-BLANC	phone:  +41/21 785 8713
1000 LAUSANNE 26		FAX:	  +41/21 785 9486
SWITZERLAND			e-mail: rainer.warth at rdls.nestle.com

Dr. Rainer Warth
Research Scientist Bioinformatics

BioAnalytical Science Department
Nestlé Research Center
Vers-Chez-LES-BLANC	phone:  +41/21 785 8713
1000 LAUSANNE 26		FAX:	  +41/21 785 9486
SWITZERLAND			e-mail: rainer.warth at rdls.nestle.com