Beispiel #1
0
        private static void PlainSearch(string src, string sub)
        {
            RkSearch rksearch = new RkSearch();
            SimpleSearch ssearch = new SimpleSearch();
            DumbSearch dsearch = new DumbSearch();

            DateTime start, end;
            int idx = 0;

            Console.WriteLine("Searching");
            Console.WriteLine("Dumb Search ... ");
            start = DateTime.Now;
            idx = dsearch.Search(src, sub);
            end = DateTime.Now;
            Console.WriteLine("Dumb Search Time: {0}ms", (end - start).TotalMilliseconds);
            Console.WriteLine("Index: {0}", idx);

            Console.WriteLine("Simple Search ... ");
            start = DateTime.Now;
            idx = ssearch.Search(src, sub);
            end = DateTime.Now;
            Console.WriteLine("Simple Search Time: {0}ms", (end - start).TotalMilliseconds);
            Console.WriteLine("Index: {0}", idx);

            Console.WriteLine("Rabin Karp Search ... ");
            start = DateTime.Now;
            idx = rksearch.Search(src, sub);
            end = DateTime.Now;
            Console.WriteLine("RK Search Time: {0}ms", (end - start).TotalMilliseconds);
            Console.WriteLine("Index: {0}", idx);
        }
Beispiel #2
0
        public void RkSimpleSearchCompareTest()
        {
            RkSearch rksearch = new RkSearch();
            SimpleSearch ssearch = new SimpleSearch();

            SeqUtils gen = new SeqUtils();
            string src = gen.GenerateSequence(1000);

            string sub = src.Substring(850, 15);
            int idx = 0;

            Console.WriteLine(src.Length);

            DateTime start, end;

            start = DateTime.Now;
            idx = ssearch.Search(src, sub);
            end = DateTime.Now;
            Console.WriteLine("Simple Search Time: {0}ms", (end - start).TotalMilliseconds);
            Console.WriteLine("Index: {0}", idx);

            start = DateTime.Now;
            idx = rksearch.Search(src, sub);
            end = DateTime.Now;

            Console.WriteLine("RK Search Time: {0}ms", (end - start).TotalMilliseconds);
            Console.WriteLine("Index: {0}", idx);
        }
Beispiel #3
0
        public void RkSearchTestset()
        {
            RkSearch search = new RkSearch();
            ulong x = 25223;
            int c = search.CountSetPairs2(x);
            Assert.AreEqual(c, 6);

            x = 10578;
            c = search.CountSetPairs2(x);
            Assert.AreEqual(c, 6);
        }
Beispiel #4
0
 public void RkSearchTestSetMany()
 {
     RkSearch search = new RkSearch();
     for (ulong i = ulong.MaxValue - 20000000; i > ulong.MaxValue - 4000; i--)
     {
         Console.WriteLine(i);
         int c1 = search.CountSetPairs(i);
         int c2 = search.CountSetPairs2(i);
         Console.WriteLine("C1: {0} C2: {1}", c1, c2);
         Assert.AreEqual(c1, c2);
     }
 }
Beispiel #5
0
        public void RkSearchRandomSequence()
        {
            SeqUtils gen = new SeqUtils();
            string src = gen.GenerateSequence(1000);

            // 13 is the  max limit due to size of long
            string sub = src.Substring(900, 23);
            RkSearch search = new RkSearch();
            int idx = search.Search(src, sub);
            Assert.IsTrue(idx > 0);
            Assert.IsTrue(idx == 900);
        }
Beispiel #6
0
        private static void BasicDemo()
        {
            RkSearch rksearch = new RkSearch();
            SimpleSearch ssearch = new SimpleSearch();
            DumbSearch dsearch = new DumbSearch();

            SeqUtils gen = new SeqUtils();
            int seqLen = 200000000;
            Console.Write("Generating sequence of length {0} ....", seqLen);
            string src = gen.GenerateSequence(200000000);
            Console.WriteLine("Done.");

            int subPos = 85000001;
            int subLen = 25;
            Console.WriteLine("Substring of length {0} and at position {1}", subLen, subPos);
            string sub = src.Substring(85000001, 25);

            PlainSearch(src, sub);

            int diff = 4;
            sub = gen.InsertDiff(sub, diff);
            DiffSearch(src, sub, diff);
        }
Beispiel #7
0
        public void RkSearchTest()
        {
            string src = "acgtaaactgggacct";
            string sub = "ctg";
            RkSearch search = new RkSearch();
            int idx = search.Search(src, sub);
            Assert.IsTrue(idx > 0);
            Assert.IsTrue(idx == 7);
            Console.WriteLine("Found at {0}", idx);

            sub = "a";
            idx = search.Search(src, sub);
            Assert.IsTrue(idx >= 0);
            Assert.IsTrue(idx == 0);

            sub = "acct";
            idx = search.Search(src, sub);
            Assert.IsTrue(idx >= 0);
            Assert.IsTrue(idx == src.Length - sub.Length);

            sub = "tttt";
            idx = search.Search(src, sub);
            Assert.IsTrue(idx < 0);
        }
Beispiel #8
0
        private static void ThreeBillionRkSearch()
        {
            RkSearch rksearch = new RkSearch();
            SeqUtils util = new SeqUtils();
            SimpleSearch ssearch = new SimpleSearch();

            // We generate really large strings, which total up to 3 billion in the end.
            // The substring which we are searching for is 27 characters in length

            string sub = util.GenerateSequence(27);
            List<int> rkmatch = new List<int>();
            List<int> ssmatch = new List<int>();
            TimeSpan rkspan = TimeSpan.Zero, sspan = TimeSpan.Zero;
            DateTime start, end;

            for (int i = 0; i < 10; i++)
            {
                Console.WriteLine("Iteration {0}", i);
                for (int j = 0; j < 3000; j++)
                {
                    string src = util.GenerateSequence(1000000);
                    start = DateTime.Now;
                    rkmatch.AddRange(rksearch.SearchWithDiffAll(src, sub, 5));
                    end = DateTime.Now;

                    rkspan += (end - start);

                    start = DateTime.Now;
                    ssmatch.AddRange(ssearch.SearchWithDiffAll(src, sub, 5));
                    end = DateTime.Now;

                    sspan += (end - start);

                    src = null;
                }
            }

            Console.WriteLine("Rabin Karp Time taken: {0} s", rkspan.TotalSeconds);
            for (int i = 0; i < rkmatch.Count; i++)
            {
                Console.WriteLine(rkmatch[i]);
            }

            Console.WriteLine("Simple Search Time Taken: {0} s", sspan.TotalSeconds);
            for (int i = 0; i < rkmatch.Count; i++)
            {
                Console.WriteLine(ssmatch[i]);
            }

            bool equal = true;
            for (int i = 0; i < rkmatch.Count; i++)
            {
                if (rkmatch[i] != ssmatch[i])
                {
                    equal = false;
                    break;
                }
            }

            Console.WriteLine("Rabin Karp and Simple Search matches are equal: {0}", equal);
        }
Beispiel #9
0
        public void RkSearchWithDiff()
        {
            SeqUtils util = new SeqUtils();
            string src = util.GenerateSequence(1000);
            string sub = src.Substring(900, 23);
            RkSearch search = new RkSearch();
            sub = util.InsertDiff(sub, 5);

            int idx = search.SearchWithDiff(src, sub, 5);
            Assert.IsTrue(idx > 0);
        }