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
[EMAIL PROTECTED]
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/AceSequence.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/AceSequence.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/AceSequenceDB.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/AceSequenceDB.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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