[Biojava-dev] build failure strangeness: bogus errors

[Keith James]

I've got build failures on a fresh checkout since the projection
changes (identical to Sylvian's):

compile:
    [javac] Compiling 1069 source files to /nfs/team81/kdj/dev/biojava-live/ant-build
/classes/main
    [javac] /nfs/team81/kdj/dev/biojava-live/ant-build/src/main/org/biojava/bio/seq/i
mpl/RevCompSequence.java:47: reference to ProjectedFeatureHolder is ambiguous, both c
lass org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.pro
jection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq m
atch
    [javac]     private ProjectedFeatureHolder pfh;
    [javac]             ^
    [javac] /nfs/team81/kdj/dev/biojava-live/ant-build/src/main/org/biojava/bio/seq/i
mpl/RevCompSequence.java:63: reference to ProjectedFeatureHolder is ambiguous, both c
lass org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.pro
jection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq m
atch
    [javac]         pfh = new ProjectedFeatureHolder(new TranslateFlipContext(seq,thi
s,seq.length()+1,true));
    [javac]                   ^
    [javac] /nfs/team81/kdj/dev/biojava-live/ant-build/src/main/org/biojava/bio/seq/S
equenceTools.java:90: cannot resolve symbol
    [javac] symbol  : constructor SubSequence (org.biojava.bio.seq.Sequence,int,int,j
ava.lang.String)
    [javac] location: class org.biojava.bio.seq.SubSequence
    [javac]     return new SubSequence(seq, start, end, name);
    [javac]            ^
    [javac] 3 errors

Looking at the code, I don't think this should be happening. If I
change the imports on RevCompSequence so that I explictly import the
required classes from seq.projection before I do an import on demand
from seq then RevCompSequence will compile.

The SubSequence error is also bogus because this public constructor
does exist. If I do explicit imports again this also goes away.

I'm not sure what the underling cause of this is - any ideas?

maul[kdj]~/dev/biojava-live: uname -a
OSF1 maul V5.1 2650 alpha

maul[kdj]~/dev/biojava-live: java -version
java version "1.4.1"
Java(TM) 2 Runtime Environment, Standard Edition
Fast VM (build 1.4.1-1, native threads, mixed mode, 02/26/2003-14:52)

-- 

- Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -