[Biojava-l] Source dist corrupted?

[hilmar.lapp@pharma.Novartis.com]

Dear all,

maybe no-one of you is using the source distribution packaged as .tar.gz from
the download
area the web site points to, but that's what I did today (already the 2nd
attempt), and I failed to compile (build) the classes (I'm using a Java 1.2.2
port on Irix) because some files seem to be missing from the distribution:

[...]
src/org/biojava/bio/dp/FlatModel.java:39: Superclass
org.biojava.bio.dp.ModelView of class org.biojava.bio.dp.FlatModel not found.
public class FlatModel extends ModelView {
                               ^
src/org/biojava/bio/dp/FlatModel.java:322: Superclass
org.biojava.bio.dp.StateView of nested class org.biojava.bio.dp.FlatModel.
EmissionWrapper not found.
  extends StateView
          ^
src/org/biojava/bio/seq/tools/SimpleCrossProductAlphabet.java:40: Interface
org.biojava.bio.seq.tools.CrossProductAlphabet of class
org.biojava.bio.seq.tools.SimpleCrossProductAlphabet not found.
class SimpleCrossProductAlphabet implements FiniteAlphabet, CrossProductAlphabet
{
[... lots of further errors deleted]

The classes seem to present in the jar which is also provided for download. I'm
wondering
whether you expect people to either get the jar or fetch their own CVS tree. CVS
is not an
option for me because I can't get through our firewall.

Second, while I skimmed through the mail archive, I noticed that apparently you
recently
renamed some of the core classes (like ResidueList), and moved others. Maybe I
misunderstood
this, but if not, would it mean, that the current API will partially become
invalid in the very next distribution, or already is in the current CVS
controlled repository. That is, how
stable is the API, and if it is still unstable but at least parts have already
settled, how can one discriminate between these.

Cheers,

     Hilmar


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Hilmar Lapp                            email: Hilmar.Lapp@pharma.novartis.com
NFI Vienna, IFD/Bioinformatics         phone: +43 1 86634 631
A-1235 Vienna                          fax:   +43 1 86634 727
ROI: Bioinformatics (arrays, expression, seqs), Programming (OO), Databases
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