Create CallBackTest.java

POMP-DETECT/CallBackTest.java

@@ -0,0 +1,190 @@
+//package multicore;
+
+//import spliced.Analyses;
+//import spliced.Utilities;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.lang.management.ManagementFactory;
+import java.lang.management.ThreadMXBean;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.*;
+
+public class CallBackTest {
+
+    private static int NUM_OF_TASKS = 16;
+    Object result;
+    int cnt = 0;
+    long begTest, total_time;
+
+    public CallBackTest() {
+        begTest = new java.util.Date().getTime();
+        total_time = 0;
+    }
+
+    public void callBack(Object result, List<Utilities.Information> final_list) throws IOException {
+        this.result = result;
+
+        for (Utilities.Information in : final_list) {
+            if (Math.abs(in.getLeft_boundary() - in.getRight_boundary()) >=
+                    Utilities.min && Math.abs(in.getLeft_boundary() - in.getRight_boundary()) <= 200000) {
+                Utilities.informations.add(in);
+            }
+        }
+
+        long id = java.lang.Thread.currentThread().getId();
+        ThreadMXBean bean = ManagementFactory.getThreadMXBean();
+
+        if (!bean.isThreadCpuTimeSupported()) {
+            total_time += 0L;
+        }
+
+        long t = bean.getThreadCpuTime(id);
+
+        if (t != -1) {
+            total_time += t;
+        }
+
+        if (++cnt == NUM_OF_TASKS) {
+
+            try {
+                System.out.println("SLEEPING STARTED...");
+                Thread.sleep(6000);
+            } catch (InterruptedException e) {
+                e.printStackTrace();
+            }
+
+            System.out.println("SLEEPING ENDED...");
+
+            String file_name = "OUT/predicted_introns.txt";
+            String text;
+
+            FileWriter fileWriter = new FileWriter(file_name, false);
+            BufferedWriter out = new BufferedWriter(fileWriter);
+
+            for (int i = 0; i < Utilities.informations.size(); i++) {
+                Utilities.Information info = Utilities.informations.get(i);
+
+                text = info.getLeft_boundary() + "\t" + info.getRight_boundary() + "\n";
+
+                out.write(text);
+            }
+            out.close();
+
+            file_name = "OUT/junctions_information.info";
+
+            fileWriter = new FileWriter(file_name, true);
+            out = new BufferedWriter(fileWriter);
+
+            HashMap<Integer, List<Utilities.Information>> hash_map = new HashMap<Integer, List<Utilities.Information>>();
+
+            for (Utilities.Information junction : Utilities.informations) {
+
+                int read_id = junction.getContig_id();
+                int left_boundary = junction.getLeft_boundary();
+                int right_boundary = junction.getRight_boundary();
+
+
+                if (hash_map.containsKey(read_id)) {
+
+                    List<Utilities.Information> infos = hash_map.get(read_id);
+                    boolean accept = true;
+
+                    for (Utilities.Information info : infos) {
+                        int _left = info.getLeft_boundary();
+                        int _right = info.getRight_boundary();
+
+                        if (Math.abs(left_boundary - _left) <= 10 && Math.abs(right_boundary - _right) <= 10) {
+                            accept = false;
+                            break;
+                        }
+                    }
+
+                    if (accept) {
+                        infos.add(junction);
+                    }
+
+                } else {
+                    List<Utilities.Information> infos = new ArrayList<Utilities.Information>();
+                    infos.add(junction);
+                    hash_map.put(read_id, infos);
+                }
+            }
+
+            for (Object o : hash_map.entrySet()) {
+                Map.Entry entry = (Map.Entry) o;
+                List<Utilities.Information> infos = (List<Utilities.Information>) entry.getValue();
+
+                for (Utilities.Information junction : infos) {
+
+                    int read_id = junction.getContig_id();
+                    int left_mismatch = junction.getLeft_mismatch();
+                    int right_mismatch = junction.getRight_mismatch();
+                    int left_boundary = junction.getLeft_boundary();
+                    int right_boundary = junction.getRight_boundary();
+                    int left_length = junction.getLeft_length();
+                    int right_length = junction.getRight_length();
+                    int intron_length = junction.getIntron_length();
+                    int coverage = junction.isCoverage() ? 1 : 0;
+
+                    text = String.valueOf(read_id) + "\t" + String.valueOf(left_mismatch) + "\t" + String.valueOf(right_mismatch) + "\t" +
+                            String.valueOf(left_boundary) + "\t" + String.valueOf(right_boundary) + "\t" + String.valueOf(left_length) + "\t" +
+                            String.valueOf(right_length) + "\t" + String.valueOf(intron_length) + "\t" + String.valueOf(coverage) + "\n";
+
+                    out.write(text);
+                }
+            }
+
+            out.close();
+
+            Double secs = (new java.util.Date().getTime() - begTest) * 0.001;
+            System.out.println("WALL_CLOCK_RUN_TIME: " + secs + " secs");
+
+            double time_in_seconds = (double) total_time / 1000000000.0;
+            System.out.println("CPU_RUN_TIME -> " + time_in_seconds + " secs");
+
+            System.exit(0);
+        }
+
+    }
+
+    public void run(Utilities utilities) {
+
+        int nrOfProcessors = Runtime.getRuntime().availableProcessors();
+        System.out.println("PROCESSORS: " + nrOfProcessors);
+        NUM_OF_TASKS = nrOfProcessors;
+        NUM_OF_TASKS = Utilities.number_of_threads;
+
+        ExecutorService es = Executors.newFixedThreadPool(nrOfProcessors);
+        int start = 0, end = 0;
+
+        int hold = Utilities.union_list.size() / NUM_OF_TASKS;
+
+        for (int i = 0; i < NUM_OF_TASKS; i++) {
+
+            if (i == 0) {
+                start = 0;
+                end = hold;
+            } else if (i == NUM_OF_TASKS - 1) {
+                start = end + 1;
+                end = Utilities.union_list.size() - 1;
+            } else {
+                start = end + 1;
+                end = start + hold;
+            }
+
+            CallBackTask task = new CallBackTask(i, start, end, utilities);
+            task.setCaller(this);
+            es.submit(task);
+        }
+    }
+
+    public static void main(String[] args) throws IOException {
+        Utilities utilities = new Utilities("properties.prop");
+        new CallBackTest().run(utilities);
+    }
+}