[Biojava-l] Depreciated methods

[Richard Holland]

Most methods include a note saying which method should be used instead.
For those that don't, take a look in the org.biojavax packages to see if
there are suitable alternative classes.

In the case of the deprecated SeqIOTools.fileToBioJava, a much better
version of the FASTA parser/writer exists in the org.biojavax packages.
Instructions on how to use it are here:

http://www.biojava.org/wiki/BioJava:BioJavaXDocs#Example

cheers,
Richard

Hamed, Ahmed A. wrote:
> Thanks Richard!
> 
> For the deprecated methods, is there a reference or a wiki that maps the
> deprecated ones to ones that should be used instead?
> 
> As for the examples I am having trouble with: WriteToFasta is one. Here
> is the error that I am getting:
> java.lang.IllegalArgumentException: No alphabet was set in the identifier
>     at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:928)
>     at examples.WriteToFasta.main(WriteToFasta.java:43)
> 
> And here is my parameter value:
>       //get the int constant for the file type
>       int fileType = Integer.parseInt("2");
> 
> I would appreciate any help.
> Best wishes,
> Ahmed
> 
> 
> 
> 
> On Mon, Jan 26, 2009 at 3:10 AM, Richard Holland
> <holland at eaglegenomics.com <mailto:holland at eaglegenomics.com>> wrote:
> 
>     > I am new to BioJava and I have been trying some of its examples. I
>     came
>     > across some of the depreciated methods and I am not sure if they
>     will be
>     > removed entirely any time soon?
> 
>     Deprecated = may be removed without notice in any future release. I
>     couldn't say for any individual method, but in general it's a bad idea
>     to use anything that is marked deprecated when writing new code.
> 
>     > I also found some of the examples
>     > problematic and didn't run properly even though I am following the
>     > instructions stated in the comment section.
> 
>     Could you specify exactly which examples didn't work, and the exact
>     problems you had with them?
> 
>     thanks,
>     Richard
> 
>     > Please let me know if you have answers for my questions.
>     > Best wishes,
>     > Ahmed
>     >
> 
>     --
>     Richard Holland, BSc MBCS
>     Finance Director, Eagle Genomics Ltd
>     M: +44 7500 438846 | E: holland at eaglegenomics.com
>     <mailto:holland at eaglegenomics.com>
>     http://www.eaglegenomics.com/
> 
> 
> 
> 
> -- 
> Ahmed Abdeen Hamed
> Scientific Informatics Project Leader
> Marine Biological Laboratory Woods Hole, MA
> --
> Ph.D. student, Complex Systems
> School of Informatics, Indiana University
> 
> 
> 

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/