BioJava import qblast error.

Question

[Bioaln]

Hello, I've been recently trying to use the BioJava's BLAST implementation but in vain. I'm using the maven

repository yet these imports give me error:

these biojava3 imports cannot be resolved:

import biojava3-ws.target.classes.org.biojava3.ws.alignment.qblast.BlastProgramEnum;
import biojava3-ws.target.classes.org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
import biojava3-ws.target.classes.org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
import biojava3-ws.target.classes.org.biojava3.ws.alignment.qblast.NCBIQBlastService;

How do I handle this problem?

Answer 1

[Jose Manuel Duarte]

Your imports have an extra prefix, you just need to drop the biojava3-ws.target.classes and it should work:

import org.biojava3.ws.alignment.qblast.BlastProgramEnum;
import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastService;

Answer 2

[Pierre Lindenbaum]

run the following command in your directories:

find youdir1 yourdir2 mavendir  -name "*.jar" -exec jar tvf '{}' ';' | grep -F "NCBIQBlastService.class"

If find finds the class: it's a classpath problem with your program.

If it cannot find the class: it was not downloaded with maven; check your pom.xml, version, etc...