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 > <[email protected] <mailto:[email protected]>> 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: [email protected] > <mailto:[email protected]> > 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: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
