[Biojava-dev] Trouble compiling biojava demos

[Thomas Down]

Hi.

Firstly, what version of BioJava are you testing here?  From your  
command line, it looks like you're using 1.00 which is now very old  
indeed.  I'd suggest upgrading to 1.4.

How are you trying to compile the demos?  From the errors you're  
quoting, it looks like the compiler couldn't find any of the main  
BioJava classes -- have you added biojava.jar to your CLASSPATH?

        Thomas.


On 13 Sep 2005, at 03:32, GREG OMENKEUKWU wrote:

> I am new to biojava and I am having a little problem
> with the sample applications.
> I tried compiling the samples in the bioja demos but I
> keep getting the following errors. I will appreciate
> any help I get on this issue. Thanks.
> C:\biojava-1.00\demos>javac seq\TestEmbl.java
> seq\TestEmbl.java:18: cannot find symbol
> symbol  : class EmblFormat
> location: class seq.TestEmbl
>       SequenceFormat eFormat = new EmblFormat();
>                                    ^
> seq\TestEmbl.java:21: cannot find symbol
> symbol  : class SimpleSequenceFactory
> location: class seq.TestEmbl
>       SequenceFactory sFact = new
> SimpleSequenceFactory();
>                                   ^
> seq\TestEmbl.java:23: cannot find symbol
> symbol  : class SymbolParser
> location: class seq.TestEmbl
>       SymbolParser rParser = alpha.getParser("token");
>       ^
> seq\TestEmbl.java:23: cannot find symbol
> symbol  : method getParser(java.lang.String)
> location: interface org.biojava.bio.symbol.Alphabet
>       SymbolParser rParser = alpha.getParser("token");
>                                   ^
> seq\TestEmbl.java:25: internal error; cannot
> instantiate org.biojava.bio.seq.io.
> StreamReader.<init> at
> org.biojava.bio.seq.io.StreamReader to ()
>         new StreamReader(eReader, eFormat, rParser,
> sFact);
>         ^
> 5 errors
>
>
>
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