[Biojava-l] QBlast in BioJava3

[Matthew Busse]

Hello Sylvain, et al.,

I think I may have found another similar issue.

Here's my program:

package com.multiBLAST.model;

import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Set;

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

public class BLASTExample {

    public static void main(String [] args) {

        NCBIQBlastService blaster;
        NCBIQBlastOutputProperties outputProperties;
        InputStream is;
        String request = "";
        final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";
        String rid = new String();

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

            request = blaster.sendAlignmentRequest(TESTSEQUENCE,
alignmentProperties);

            System.out.println("Trying to get BLAST results for RID " +
rid);

            boolean wasBlasted = false;

            while (!wasBlasted) {
                wasBlasted = blaster.isReady(rid,
System.currentTimeMillis());
            }

            outputProperties = new NCBIQBlastOutputProperties();
            outputProperties.setOutputFormat(NCBIQBlastOutputFormat.TEXT);

outputProperties.setAlignmentOutputFormat(NCBIQBlastOutputFormat.PAIRWISE);
            outputProperties.setDescriptionNumber(10);
            outputProperties.setAlignmentNumber(10);

            //to show that output options were followed

            Set<String> test = outputProperties.getOutputOptions();

            for(String str : test) {
                System.out.println(str);
            }

            is = blaster.getAlignmentResults(request, outputProperties);

            BufferedReader br = new BufferedReader(new
InputStreamReader(is));

            String line = null;

            while ((line = br.readLine()) != null)    {
                System.out.println(line);
            }

        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }
}

When I run it, it throws an exception:
java.lang.Exception: The key named PROGRAM is not set in this
RemoteQBlastOutputProperties object
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties.getAlignmentOption(NCBIQBlastAlignmentProperties.java:173)
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendActualAlignementRequest(NCBIQBlastService.java:132)
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendAlignmentRequest(NCBIQBlastService.java:210)
    at com.multiBLAST.model.BLASTExample.main(BLASTExample.java:30)

Because RemoteQBlastOutputProperties is the terminology used in the pre-BJ3
APIs, I'm guessing this is another conversion problem? Or am I missing
something else?

Many thanks for all your help.

Best,
Matthew

On Wed, Dec 29, 2010 at 9:58 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks Sylvain,
>
> Matthew, a workaround until we have a fix for this is to add the
> http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
> from the biojava-legacy project to your classpath. This should allow
> your example to work...
>
> Andreas
>
>
> On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
> <sylvain.foisy at diploide.net> wrote:
> > Hi,
> >
> > I am the author/main culprit for the QBlast code in BJ. I have to fix the
> problem that you found ASAP to remove the dependency on the old BJ
> architecture about representing Sequence objects. I'll work on this early
> next week, as soon as I'll have finish with my grading... I am more of a
> teacher than a coder nowadays.
> >
> > Best regards
> >
> > Sylvain
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>