[Biojava-l] biojava-acedb - recent version?

[Matthew Pocock]

Hi Ben,

I don't think we ever got the ace->sequence bridge working fully. It was
done before the days of the feature projection framework, when life was even
more complicated. The package for retrieving ace objects should all work
fine though. Initialy, you could 'hide' the org.acedb.sequence package by
deleting it or moving it sideways and have a play with the client only.

I think the current ace object model is read-only, or if it allows
moddifications, it doesn't write them back to the server. This could be
fixed if you need read/write access. If you need the functionality of making
ace objects look like biojava sequences, then we can re-visit that package
and try to sort things out for you.

All the best,

Matthew

chat code at: irc.openprojects.net #biojava

----- Original Message -----
From: "Ben Oberkfell" <boberkfe@watson.wustl.edu>
To: <biojava-l@biojava.org>
Sent: Friday, April 05, 2002 12:14 AM
Subject: [Biojava-l] biojava-acedb - recent version?


>
> I've been trying to locate the biojava-acedb package, and all I've been
> able to get is from the CVS server -- however, the CVS server shows that
> these files are over a year old.
>
> I'm using v1.21 of the Biojava package, and attempted to build this and
got
> the several compiler errors, and warnings about using a deprecated API.
> (refer to the end of the message for the ant output in question)
>
> It looks as though one or two of these classes referenced do not
> exist in the source package at all (AceLinkSequence & AceRealSequence, for
> example).
>
> Any help in getting this to build properly would be greatly appreciated.
>
>
>
> Thanks,
>
>
> Ben Oberkfell
> boberkfe@watson.wustl.edu
>
>
> Here is the ant output with the errors:
> ---------------------------------------
>
>     [javac] Note: sun.tools.javac.Main has been deprecated.
>     [javac]
>
/home14/watson/boberkfe/biojava-acedb/ant-build/src/org/acedb/seq/AceSequenc
e.java:157:
> Class org.acedb.seq.SymbolParser not found.
>     [javac]       SymbolParser rParser = getAlphabet().getParser("token");
>     [javac]       ^
>     [javac]
>
/home14/watson/boberkfe/biojava-acedb/ant-build/src/org/acedb/seq/AceSequenc
e.java:157:
> Method getParser(java.lang.String) not found in interface
org.biojava.bio.symbol.Alphabet.
>     [javac]       SymbolParser rParser = getAlphabet().getParser("token");
>     [javac]                                                     ^
>     [javac]
>
/home14/watson/boberkfe/biojava-acedb/ant-build/src/org/acedb/seq/AceSequenc
eDB.java:133:
> Class org.acedb.sequence.AceLinkSequence not found.
>     [javac]           seq = new AceLinkSequence(this, (AceObject)
links.retrieve(id));
>     [javac]                     ^
>     [javac]
>
/home14/watson/boberkfe/biojava-acedb/ant-build/src/org/acedb/seq/AceSequenc
eDB.java:135:
> Class org.acedb.sequence.AceRealSequence not found.
>     [javac]           seq = new AceRealSequence((AceObject)
realSeqs.retrieve(id));
>     [javac]                     ^
>     [javac]
> /home14/watson/boberkfe/biojava-acedb/ant-build/src/org/acedb/Ace.java:97:
> Method fetch(org.acedb.AceURL) not found in interface org.acedb.Database.
>     [javac]       return db.fetch(url);
>     [javac]                      ^
>     [javac] Note: 4 files use or override a deprecated API.  Recompile
with
> "-deprecation" for details.
>     [javac] 5 errors, 2 warnings
>
>
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