BioJava import qblast error.
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0
Entering edit mode
7.0 years ago
Bioaln ▴ 350

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?

Biojava java import • 1.5k views
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1
Entering edit mode
7.0 years ago

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;

 

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0
Entering edit mode
7.0 years ago

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...

 

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