TCoffee.java Source code

Introduction

Here is the source code for TCoffee.java

Source

/*
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import java.io.BufferedReader;
import java.io.IOException;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.hbase.HBaseConfiguration;
import org.apache.hadoop.hbase.HColumnDescriptor;
import org.apache.hadoop.hbase.HTableDescriptor;
import org.apache.hadoop.hbase.client.HBaseAdmin;
import java.io.File;
import java.io.FileReader;
import org.apache.hadoop.hbase.client.HTable;
import org.apache.hadoop.hbase.client.Put;
import org.apache.hadoop.hbase.util.Bytes;

/**
 *
 * @author Albert
 */
public class TCoffee {

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws IOException {

        HBaseConfiguration hconfig = new HBaseConfiguration(new Configuration());
        System.out.println("Connecting...");
        HBaseAdmin hbase_admin = new HBaseAdmin(hconfig);
        if (!hbase_admin.tableExists("TCoffee")) {
            HTableDescriptor htable = new HTableDescriptor("TCoffee");
            htable.addFamily(new HColumnDescriptor("key"));
            htable.addFamily(new HColumnDescriptor("value"));
            System.out.println("Creating Table...");
            hbase_admin.createTable(htable);

        } else {
            hbase_admin.disableTable("TCoffee");
            hbase_admin.deleteTable("TCoffee");
            HTableDescriptor htable = new HTableDescriptor("TCoffee");
            htable.addFamily(new HColumnDescriptor("key"));
            htable.addFamily(new HColumnDescriptor("value"));
            System.out.println("Delete and creating table...");
            hbase_admin.createTable(htable);
        }
        HTable hTable = new HTable(hconfig, "TCoffee");
        BufferedReader reader = null;
        int count = 0;
        File file = new File("full_lib.txt");
        reader = new BufferedReader(new FileReader(file));
        String line = null;
        String[] seq = null;
        String[] split = null;
        boolean cond = false;
        while ((line = reader.readLine()) != null) {
            if (line.indexOf('#') >= 0) {
                line = line.replace("#", "");
                seq = line.split("\\s+");
                cond = true;
            } else if (cond && line.indexOf('!') >= 0) {
                break;
            } else if (cond) {
                split = line.split("\\s+");
                Put put = new Put(Bytes.toBytes("row" + count));
                put.addColumn(Bytes.toBytes("key"), Bytes.toBytes("seq1"), Bytes.toBytes(seq[0]));
                put.addColumn(Bytes.toBytes("key"), Bytes.toBytes("res1"), Bytes.toBytes(split[1]));
                put.addColumn(Bytes.toBytes("value"), Bytes.toBytes("seq2"), Bytes.toBytes(seq[1]));
                put.addColumn(Bytes.toBytes("value"), Bytes.toBytes("res2"), Bytes.toBytes(split[2]));
                put.addColumn(Bytes.toBytes("value"), Bytes.toBytes("pes"), Bytes.toBytes(split[3]));
                hTable.put(put);
                count++;
                put = new Put(Bytes.toBytes("row" + count));
                put.addColumn(Bytes.toBytes("key"), Bytes.toBytes("seq1"), Bytes.toBytes(seq[1]));
                put.addColumn(Bytes.toBytes("key"), Bytes.toBytes("res1"), Bytes.toBytes(split[2]));
                put.addColumn(Bytes.toBytes("value"), Bytes.toBytes("seq2"), Bytes.toBytes(seq[0]));
                put.addColumn(Bytes.toBytes("value"), Bytes.toBytes("res2"), Bytes.toBytes(split[1]));
                put.addColumn(Bytes.toBytes("value"), Bytes.toBytes("pes"), Bytes.toBytes(split[3]));
                hTable.put(put);
                count++;
            }
        }
        hTable.close();
        System.out.println("Done!");
    }
}