[Biojava-dev] Some problems with createDNASequence

[William Stott]

Hi,

 I'm just evaluating BioJava and seem to have encountered a problem:

 Sequence dna = DNATools.createDNASequence("atgctgB", "dna_1");

 I expected an exception to be thrown (see attached Unit Test) as B is not a valid character for a DNA sequence (atgc), but it wasn't.

 Do you publish the JUnit Tests for BioJava? Where can they be obtained? Is there a more formal mechanism for  submitting defect reports?

 Regards

 Will

P.S. I sent this message before, but it got bounced due to a suspicious header

 


createDNASequence

public static Sequence createDNASequence(java.lang.String dna,
                                         java.lang.String name)
                                  throws IllegalSymbolException

	Return a new DNA Sequence for dna. 

	

	

		Parameters: 
		dna - a String to parse into DNA 
		name - a String to use as the name 
		Returns: 
		a Sequence created form dna 
		Throws: 
		IllegalSymbolException - if dna contains any non-DNA characters

 

-------------- next part --------------
package BioJavaTests;

/**
 * PACKAGE_NAME
 * User: Bills Date: 17-Nov-2004 Time: 19:06:01
 * Copyright 2004 Will Stott
 */

import junit.framework.TestCase;
import junit.framework.Assert;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.IllegalSymbolException;

public class ToolsCheck extends TestCase
{

    public void testCreateGoodDNASequence() throws Exception
    {
        Sequence dna = DNATools.createDNASequence("atgct", "dna_1");
        Assert.assertEquals("atgct", dna.seqString());
    }

    public void testCreateBadDNASequence() throws Exception
    {
        try
        {
            Sequence dna = DNATools.createDNASequence("aBtgctg", "dna_1");
            throw new Exception("this should not be thrown");
        }
        catch(IllegalSymbolException e)
        {
           Assert.assertEquals("This tokenization doesn't contain character: 'B'", e.getMessage());
        }
    }


    public ToolsCheck(String test)
    {
        super(test);
    }

    protected void setUp() throws Exception
    {

    }

    protected void tearDown() throws Exception
    {

    }

}