[Biojava-dev] ViewSequence

[Matthew Berryman]

Sure, I'd love to :)

I'll have a dig through my piles of code and see what isn't covered in 
the biojava in anger site and send them somewhere (where?).
I should mention I'm in the middle of debugging some biojava 
distribution weirdness, where training works/not works depending on the 
order the distributions are created and registered with a 
SimpleDistributionTrainerContext.. anyone seen this behaviour? I'll 
post to the list sometime soon with more info, once I've tracked down 
the bug some more.

Cheers,
Matt.

On 05/03/2004, at 14:34, mark.schreiber at group.novartis.com wrote:

> If anyone wants to contribute pages, programs or corrections to 
> biojava in
> anger then I would be more than pleased to put them on the site and 
> give
> appropriate credit. Simple examples are fine, you don't need to make a
> killer app or anything. Unfortunately I am often too busy to keep these
> pages as up to date or as complete as I would like.
>
> International fame awaits :)
>
> - Mark
>
>
>
>
>
>
> Matthew Berryman <mattjb at eleceng.adelaide.edu.au>
> Sent by: biojava-dev-bounces at portal.open-bio.org
> 03/05/2004 11:44 AM
>
>
>         To:     "Warth,Rainer,LAUSANNE,NRC/BAS" 
> <rainer.warth at rdls.nestle.com>
>         cc:     "'biojava-dev at biojava.org'" <biojava-dev at biojava.org>
>         Subject:        Re: [Biojava-dev] ViewSequence
>
>
> BioJava in Anger pages are out of date...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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>>
>
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