org.apache.commons.lang.mutable.MutableFloat Java Examples

public void createReview(final Review reviewRequest, final List<Review.File.Comment> comments, String reviewComment,
                         final Progress progress) throws Exception {
    final RBReview review = client.createReviewApi(reviewRequest.id, null);
    final MutableFloat progressF = new MutableFloat(0f);

    for (final Review.File.Comment comment : comments) {
        progress.progress("Updating comment", progressF.floatValue());
        client.createDiffComment(reviewRequest.id, String.valueOf(review.review.id),
                comment.file.fileId, comment.firstLine, comment.numberOfLines, comment.text, comment.issueOpened);
        progressF.setValue(progressF.floatValue() + 1.0f / (comments.size() - 1));
    }

    progress.progress("Making review public", progressF.floatValue());
    client.updateReviewApi(reviewRequest.id, String.valueOf(review.review.id), true, reviewComment, null);
    progress.progress("Review Completed", 1);
}
 

private static Pair<String, String> consensusSeq(String s1, String s2, String qual1, String qual2, int maxMismatches,
		MutableFloat mismatchFrac) {
	StringBuffer consensus = new StringBuffer();
	StringBuffer consensusQual = new StringBuffer();
	int numMismatches = 0;
	
	for (int i=0; i<s1.length(); i++) {
		if (s1.charAt(i) != s2.charAt(i)) {

			numMismatches += 1;
			if (numMismatches > maxMismatches) {
				return null;
			} else {
				if (qual1.charAt(i) >= qual2.charAt(i) + 10) {
					consensus.append(s1.charAt(i));
					consensusQual.append(qual1.charAt(i));
				} else if (qual2.charAt(i) >= qual1.charAt(i) + 10) {
					consensus.append(s2.charAt(i));
					consensusQual.append(qual2.charAt(i));						
				} else {
					consensus.append('N');
					consensusQual.append('!');
				}
			}
			
		} else {
			consensus.append(s1.charAt(i));
			consensusQual.append((char) Math.max(qual1.charAt(i), qual2.charAt(i))); 
		}
	}
	
	mismatchFrac.setValue((float) numMismatches / (float) s1.length());
	
	return new Pair<String,String>(consensus.toString(), consensusQual.toString());
}
 

private void updateLogLikBestModel(JobConf conf, int niter,  Map<String, LinearModel> z, String testPath, 
                                  boolean ignoreValue, MutableFloat bestTestLoglik, String outBasePath, 
                                  int  numClickReplicates) throws IOException
{   
  Map<String, Double> loglik;
  loglik = testloglik(conf, z, testPath, 1, ignoreValue);
  
  AvroHdfsFileWriter<GenericRecord> writer =
      new AvroHdfsFileWriter<GenericRecord>(conf, outBasePath
          + "/sample-test-loglik/iteration-"+niter +".avro", SampleTestLoglik.SCHEMA$);
  DataFileWriter<GenericRecord> testRecordWriter = writer.get();  

  for (String k : z.keySet())
  {     
    GenericData.Record valuemap = new GenericData.Record(SampleTestLoglik.SCHEMA$);
    valuemap.put("iter", niter);
    valuemap.put("testLoglik", loglik.get(k).floatValue());
    valuemap.put("lambda", k);
    testRecordWriter.append(valuemap);
    _logger.info("Sample test loglik for lambda=" + k + " is: "
        + String.valueOf(loglik.get(k)));
   
    // output best model up to now
    if (loglik.get(k) > bestTestLoglik.floatValue() && niter>0)
    {
      String bestModelPath = outBasePath + "/best-model/best-iteration-" + niter + ".avro";
      FileSystem fs = FileSystem.get(conf);
      fs.delete(new Path(outBasePath + "/best-model"), true);
      LinearModelUtils.writeLinearModel(conf, bestModelPath, z.get(k), k);
      bestTestLoglik.setValue(loglik.get(k).floatValue());
    }
  }
  testRecordWriter.close();
}
 

public List<Review.File> files(final Review review, final Progress progress) throws Exception {
    List<Review.File> result = new ArrayList<>();
    final List<Future> futures = new CopyOnWriteArrayList<>();
    final MutableFloat progressF = new MutableFloat(0f);
    final RBDiffList diffList = client.diffListApi(review.id);

    if (diffList.total_results > 0) {
        final String revision = String.valueOf(diffList.diffs[0].revision);
        final RBFileDiff fileDiff = client.fileDiffApi(review.id, revision);

        for (final RBFileDiff.File file : fileDiff.files) {
            final Review.File diffFile = new Review.File();

            diffFile.fileId = file.id;
            diffFile.srcFileName = file.source_file;
            diffFile.dstFileName = file.dest_file;
            diffFile.sourceRevision = file.source_revision;
            diffFile.revision = revision;

            futures.add(ApplicationManager.getApplication().executeOnPooledThread(
                    new Runnable() {
                        @Override
                        public void run() {
                            progress.progress("Loading file contents "
                                    + FilenameUtils.getName(diffFile.srcFileName), progressF.floatValue());
                            diffFile.srcFileContents = client.contents(file.links.original_file.href);
                            progressF.setValue(progressF.floatValue() + 1.0f / diffList.total_results);
                            progress.progress("Completed loading contents", progressF.floatValue());
                        }
                    }
            ));

            futures.add(ApplicationManager.getApplication().executeOnPooledThread(
                    new Runnable() {
                        @Override
                        public void run() {
                            progress.progress("Loading file contents "
                                    + FilenameUtils.getName(diffFile.dstFileName), progressF.floatValue());
                            diffFile.dstFileContents = client.contents(file.links.patched_file.href);
                            progressF.setValue(progressF.floatValue() + 1.0f / diffList.total_results);
                            progress.progress("Completed loading contents", progressF.floatValue());
                        }
                    }
            ));
            result.add(diffFile);
        }
    }
    for (Future future : futures) future.get();
    return result;
}