[Biojava-l] newbie vowes pleas help me!

[Sigmund, Ralf]

newbie vowes:
i am trying to run the tutorial example GCContent.java 

using win 2k, jdk 1.3 and having a directory c:\biotest like this: 


 Directory of C:\biotest

 03.08.2000  19:13       <DIR>          .
 03.08.2000  19:13       <DIR>          ..
 01.08.2000  08:42              536.372 biojava.jar
 03.08.2000  18:09                  356 ClassName.java
 03.08.2000  18:09                  279 filesystem.attributes
 03.08.2000  18:10                1.267 GCContent.java
 15.06.2000  14:53              145.710 xml.jar
                5 File(s)        683.984 bytes
                2 Dir(s)     407.945.216 bytes free

, 


the command :

c:\jdk1.3\bin\javac.exe -classpath c:/biotest/biojava.jar;c:/biotest/xml.jar
c:/biotest/GCContent.java

results in the following errors:
----------------------------------------------------------------------------
-----------
----------------------------------------------------------------------------
-------
c:/biotest/GCContent.java:16: cannot resolve symbol
symbol  : variable DNATools  
location: class GCContent
	Alphabet dna = DNATools.getDNA();
                       ^
c:/biotest/GCContent.java:20: cannot resolve symbol
symbol  : class SequenceFactory  
location: class GCContent
	SequenceFactory fact = new SimpleSequenceFactory();
        ^
c:/biotest/GCContent.java:20: cannot resolve symbol
symbol  : class SimpleSequenceFactory  
location: class GCContent
	SequenceFactory fact = new SimpleSequenceFactory();
                                   ^
c:/biotest/GCContent.java:29: cannot resolve symbol
symbol  : class Sequence  
location: class GCContent
	    Sequence seq = stream.nextSequence();
            ^
c:/biotest/GCContent.java:33: cannot resolve symbol
symbol  : variable DNATools  
location: class GCContent
		if (sym == DNATools.g() || sym == DNATools.c())
                           ^
c:/biotest/GCContent.java:33: cannot resolve symbol
symbol  : variable DNATools  
location: class GCContent
		if (sym == DNATools.g() || sym == DNATools.c())
                                                  ^
6 errors
--------------------------------------------------
the source again:
_______________________________

import java.io.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.io.*;

public class GCContent {
    public static void main(String[] args)
        throws Exception
    {
        if (args.length != 1)
	    throw new Exception("usage: java GCContent filename.fa");
	String fileName = args[0];
       
	// Set up stream reader

	Alphabet dna = DNATools.getDNA();
	SymbolParser dnaParser = dna.getParser("token");
	BufferedReader br = new BufferedReader(
			        new FileReader(fileName));
	SequenceFactory fact = new SimpleSequenceFactory();
	StreamReader stream = new StreamReader(br,
					       new FastaFormat(),
					       dnaParser,
					       fact);

	// Iterate over all sequences in the stream

	while (stream.hasNext()) {
	    Sequence seq = stream.nextSequence();
	    int gc = 0;
	    for (int pos = 1; pos <= seq.length(); ++pos) {
		Symbol sym = seq.symbolAt(pos);
		if (sym == DNATools.g() || sym == DNATools.c())
		    ++gc;
	    }
	    System.out.println(seq.getName() + ": " + 
			       ((gc * 100.0) / seq.length()) + 
			       "%");
	}
    }			       
}
--------------------------------------------------------

I would be grateful for any hints!
Thanxx Ralf 



Ralf Sigmund