Exemplo n.º 1
0
 // delete random directory
 protected void cleanup(Context context) throws IOException, InterruptedException {
   Iterator<DataPair> it = tree.iterator();
   while (it.hasNext()) {
     DataPair dp = it.next();
     context.write(new DoubleWritable(dp.getLigandDouble()), dp);
   }
   fo.deleteDir(new File("/home/hadoop/vinaJob/" + tmpPath));
 }
Exemplo n.º 2
0
 // topK sort,write the result to hdfs
 public void reduce(DoubleWritable key, Iterable<DataPair> values, Context context)
     throws IOException, InterruptedException {
   for (DataPair val : values) {
     if (count < k) {
       hf.createNewHDFSFile(val.getLigandPath(), val.getVinaResult());
       hf.createNewHDFSFile(val.getLogPath(), val.getVinaLog());
       int position = val.getLigandPath().lastIndexOf("/");
       String ligandName = val.getLigandPath().substring(position + 1);
       context.write(new DoubleWritable(val.getLigandDouble()), new Text(ligandName));
       /*  context.write(new DoubleWritable(val.getLigandDouble()),
       new Text(val.getLigandPath()));*/
       count++;
     } else {
       break;
     }
   }
 }
Exemplo n.º 3
0
 /*
  * (non-Javadoc)
  *
  * @see org.apache.hadoop.mapreduce.Mapper#setup(org.apache.hadoop.mapreduce.Mapper.Context)
  */
 public void setup(Context context) throws IOException, InterruptedException {
   conf = context.getConfiguration();
   conf2HDFS = conf.get("conf2HDFS");
   receptorHDFS = conf.get("receptorHDFS");
   seed = conf.get("seed");
   vinaJobID = conf.get("vinaJobID");
   k = conf.getInt("k", 1000);
   hf = new HadoopFile();
   fo = new FileOperation();
   tmpPath = fo.randomString();
   conf2Local =
       "/home/hadoop/vinaJob/"
           + tmpPath
           + "/"
           + conf2HDFS.substring(conf2HDFS.lastIndexOf("/") + 1);
   receptorLocal =
       "/home/hadoop/vinaJob/"
           + tmpPath
           + "/"
           + receptorHDFS.substring(receptorHDFS.lastIndexOf("/") + 1);
   hf.HadoopToLocal(conf2HDFS, conf2Local);
   hf.HadoopToLocal(receptorHDFS, receptorLocal);
 }
Exemplo n.º 4
0
 protected void setup(Context context) throws IOException, InterruptedException {
   Configuration conf = context.getConfiguration();
   hf = new HadoopFile();
   k = conf.getInt("k", 1000);
 }