[Biojava-l] QBlast in BioJava3

[Matthew Busse]

Hello BioJava community,

I'm a biologist/Java newbie, I'm trying to write a program that automates
BLAST requests using very short peptide sequences. I downloaded the new
BioJava 3 jars, and attempted to write the program, but I quickly ran into a
problem.

Here's the code I have so far:
package com.multiBLAST.model;

import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastService;
import org.biojava3.core.sequence.*;

public class BLASTExample {

    public static void main(String [] args) {

        NCBIQBlastService blaster;
        NCBIQBlastAlignmentProperties alignmentProperties;
        String request = "";
        final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";

        try {
            blaster = new NCBIQBlastService();
            alignmentProperties = new NCBIQBlastAlignmentProperties();
            alignmentProperties.setBlastProgram("blastp");
            alignmentProperties.setBlastDatabase("nr");

            request = blaster.sendAlignmentRequest(TESTSEQUENCE,
alignmentProperties);

        }

    }

}

Eclipse is telling me that last line of code causes a compiler error: "The
type org.biojavax.bio.seq.RichSequence cannot be resolved. It is indirectly
referenced from required .class files"

I'm not sure exactly what this means, it seems to me that perhaps when this
method was updated from biojavax to biojava3, it somewhere still references
the RichSequence from biojavax. I can't find a RichSequence class anywhere
in the new BioJava3 API, and I can't find the biojavax jars on the legacy
download page, so I'm not sure how to proceed.

If someone could please provide some assistance, that would be great.

Thank you very much,

Matthew Busse, PhD