Hi Matthew,
Let me dive in this code again and I'll find the bug. Any rush on this? I am
planning to do this early next week/year ;-) You are actually the first
reported user of this module beside me! I mostly tested it with nucleotide
sequences on the old architecture. Not much work done wince moving to the new
code base...
Back to you ASAP
Best regards
Sylvain
On 2010-12-29, at 4:01 PM, Matthew Busse wrote:
> 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 <[email protected]> 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.
> <[email protected]> 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 - [email protected]
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
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