added a UF test for bcalm

gatb-core/test/unit/src/bcalm/TestBcalm.cpp

@@ -0,0 +1,125 @@
+/*****************************************************************************
+ *   GATB : Genome Assembly Tool Box
+ *   Copyright (C) 2014  R.Chikhi, G.Rizk, E.Drezen
+ *
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Affero General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Affero General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Affero General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*****************************************************************************/
+
+#include <CppunitCommon.hpp>
+
+#include <gatb/system/impl/System.hpp>
+
+#include <gatb/tools/math/LargeInt.hpp>
+
+#include <gatb/tools/collections/impl/IteratorFile.hpp>
+
+#include <gatb/tools/misc/api/StringsRepository.hpp>
+#include <gatb/tools/misc/impl/TimeInfo.hpp>
+
+#include <gatb/bcalm2/unionFind.hpp>
+
+#include <gatb/tools/designpattern/impl/Command.hpp>
+#include <gatb/tools/designpattern/impl/IteratorHelpers.hpp>
+
+#include <iostream>
+#include <thread>
+
+using namespace std;
+
+using namespace gatb::core::tools::misc;
+using namespace gatb::core::tools::misc::impl;
+
+using namespace gatb::core::tools::dp;
+using namespace gatb::core::tools::dp::impl;
+
+using namespace gatb::core::system;
+using namespace gatb::core::system::impl;
+
+using namespace gatb::core::tools::math;
+using namespace gatb::core::tools::dp;
+using namespace gatb::core::tools::collections::impl;
+
+extern std::string DBPATH (const string& a);
+
+/********************************************************************************/
+namespace gatb  {  namespace tests  {
+/********************************************************************************/
+
+/** \brief Test class for genomic databases management
+ */
+class TestBcalm : public Test
+{
+    /********************************************************************************/
+    CPPUNIT_TEST_SUITE_GATB (TestBcalm);
+
+        CPPUNIT_TEST_GATB (bcalm_test1); 
+        CPPUNIT_TEST_SUITE_GATB_END();
+
+public:
+
+    /********************************************************************************/
+    void setUp    ()  {}
+    void tearDown ()  {}
+
+
+    /********************************************************************************/
+    void bcalm_test1 () // i wanna test de UF because it was buggy in multithreads
+    {
+        int nb_uf_elts = 3000000;
+        unionFind<uint32_t> uf(nb_uf_elts);
+
+
+        auto doJoins = [&uf](int start, int end)
+        {
+            for (int i = start; i < end; i++)
+            {
+                uf.union_(i,i+1);
+                //std::cout << "joining " << i << " " << i+1 << std::endl; // it's indeed threaded, this checks it
+            }
+
+        };
+
+        //doJoins(0,nb_uf_elts/2);
+        //doJoins(nb_uf_elts/2,nb_uf_elts-1);
+        //
+        std::thread first(doJoins,0,nb_uf_elts/3);
+        std::thread second(doJoins,nb_uf_elts/3,2*(nb_uf_elts/3));
+        std::thread third(doJoins,2*(nb_uf_elts/3),nb_uf_elts-1);
+
+        first.join();
+        second.join();
+        third.join();
+
+        int foundclass = uf.find(0); // not always 0, depends which thread starts first
+        for (int i = 1; i < nb_uf_elts; i++)
+        {   
+            int ufclass = uf.find(i);
+            if (ufclass != foundclass)
+                std::cout<< "\nclass of " << i << " is " << ufclass <<std::endl;
+            CPPUNIT_ASSERT (ufclass == foundclass);
+        }
+
+    }
+
+};
+
+/********************************************************************************/
+
+CPPUNIT_TEST_SUITE_REGISTRATION      (TestBcalm);
+CPPUNIT_TEST_SUITE_REGISTRATION_GATB (TestBcalm);
+
+/********************************************************************************/
+} } /* end of namespaces. */
+/********************************************************************************/
+