[Biojava-dev] ViewSequence

[mark.schreiber at group.novartis.com]

Hi Warth,

This page needs updateing. As of BioJava 1.3.1 ViewSequence was moved to 
org.biojava.bio.seq.impl.
Actually the recommended way to create a ViewSequence as of BJ1.3.1 and 
later is to use SequenceTools.view(sequence, newName);

My Bad :(

- Mark





"Warth,Rainer,LAUSANNE,NRC/BAS" <rainer.warth at rdls.nestle.com>
Sent by: biojava-dev-bounces at portal.open-bio.org
02/24/2004 03:40 PM

 
        To:     "'biojava-dev at biojava.org'" <biojava-dev at biojava.org>
        cc: 
        Subject:        [Biojava-dev] ViewSequence


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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