[Biojava-l] Source dist corrupted?

[Matthew Pocock]

I am just about to post today's build to the FTP site, and also update the README. I
will post once this is done.

Matthew

hilmar.lapp@pharma.Novartis.com wrote:

> 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
>
> -----------------------------------------------------------------------------
> 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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