CallBackTask.java

//package multicore;

//import spliced.Utilities;

import java.io.IOException;
import java.lang.management.ManagementFactory;
import java.lang.management.ThreadMXBean;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.Callable;

public class CallBackTask implements Callable {
    private CallBackTest callBackTest;
    private int seq;
    public Utilities utilities;
    public int start, end;

    public CallBackTask() {
    }

    public CallBackTask(int i, int start, int end, Utilities utilities) {
        this.utilities = utilities;
        seq = i;
        this.start = start;
        this.end = end;
    }

    public static long getCpuTime() {
        ThreadMXBean bean = ManagementFactory.getThreadMXBean();
        return bean.isCurrentThreadCpuTimeSupported() ? bean.getCurrentThreadCpuTime() : 0L;
    }

    public Object call() throws IOException {

        long startCpuTimeNano = getCpuTime();

        long begTest = new java.util.Date().getTime();
        System.out.println("STARTING TASK: " + seq);

        List<Utilities.Information> final_list = new ArrayList<Utilities.Information>(25000);

        try {

            int count = 0, hamming_distance, index, min_length;

            for (int i = start; i <= end; i++) {

                if(i == Utilities.union_list.size()){
                    break;
                }

                index = Utilities.union_list.get(i);
                String read = Utilities.reads.get(index);

                Utilities.reads.set(index, "");

                if (Utilities.hash_map_one.containsKey(index) && Utilities.hash_map_two.containsKey(index)) {

                    List<Utilities.Information> info_list = utilities.processUMR(index, read.length());

                    final_list.addAll(info_list);

                    info_list.clear();

                } else {

                    hamming_distance = 0;
                    min_length = 10;

                    List<Utilities.UMRInfo> list = utilities.PreProcessUMR(index, read);

                    if (list.size() > 0) {

                        List<Utilities.Information> info_list = utilities.processUMR(list, hamming_distance,
                                min_length, index, read.length());

                        if (info_list.size() <= 0) {

                            min_length = 8;

                            info_list = utilities.processUMR(list, hamming_distance, min_length, index, read.length());
                        }

                        final_list.addAll(info_list);
                    }
                }

                count++;

                if (count % 1000 == 0) {

                    System.out.println("COMPLETED " + count + " BY " + seq + " [" + final_list.size() + "]");

                    long taskCpuTimeNano = getCpuTime() - startCpuTimeNano;
                    double time_in_seconds = (double) taskCpuTimeNano / 1000000000.0;

                    Double secs = (new java.util.Date().getTime() - begTest) * 0.001;
                    System.out.println("TASK - " + seq + " TOOK " + time_in_seconds + " SECONDS");
                }
            }
        } catch (Exception x) {
            x.printStackTrace();
            System.out.println(x.getMessage());
        }

        callBackTest.callBack(seq, final_list);

        long taskCpuTimeNano = getCpuTime() - startCpuTimeNano;
        double time_in_seconds = (double) taskCpuTimeNano / 1000000000.0;

        Double secs = (new java.util.Date().getTime() - begTest) * 0.001;
        System.out.println("TASK - " + seq + " TOOK " + time_in_seconds + " SECONDS");
        return null;
    }

    public void setCaller(CallBackTest callBackTest) {
        this.callBackTest = callBackTest;
    }

    public CallBackTest getCaller() {
        return callBackTest;
    }
}