[Biojava-dev] ViewSequence

[Matthew Berryman]

BioJava in Anger pages are out of date...
ViewSequence has moved to org.biojava.bio.seq.impl, and thus the import 
line
import org.biojava.bio.seq.impl.*;

should be added or equivalent changes made to reflect the shift. I can 
only guess that this then causes the problem with writeFasta, which 
should be able to take a PrintStream and a ViewSequence according to 
the 1.3 API, it works fine in 1.4...

Matthew Berryman
BSc (Maths & Comp. Sc.)
BE (Comp. Sys.) Honours I
PhD student @ Centre for Biomedical Engineering
The University of Adelaide


On 24/02/2004, at 18:10, Warth,Rainer,LAUSANNE,NRC/BAS wrote:

> 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
>
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>