#include "geneorder.h"
#include <algorithm>
+#include <set>
#include <cstdlib>
using namespace std;
}
return v;
}
+
+int countCycles(const GeneOrder& go){
+ int cycles = 0;
+ set<size_t> marked;
+ for (size_t p = 1; p < go.size() - 1; ++p){
+ if (marked.find(p) != marked.end())
+ continue;
+ }
+ return cycles;
+}
+
+std::vector<Component> findComponents(const GeneOrder& go){
+ return vector<Component>();
+}
+
+std::vector<Interval> findIntervals(const GeneOrder& go){
+ return vector<Interval>();
+}
class GeneOrder;
+struct Component{
+ Component(int b,int e,int s):begin(b),end(e),sign(s){}
+ int begin;
+ int end;
+ int sign;
+};
+typedef std::pair<size_t,size_t> Interval;
+
/**
* Returns the length of the longest increasing sequence and the longest
* decreasing sequence.
*/
std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go);
+/**
+ * Counts the number of cycles in the gene order.
+ */
+int countCycles(const GeneOrder& go);
+
+/**
+ * Finds the components in the gene order.
+ */
+std::vector<Component> findComponents(const GeneOrder& go);
+
+/**
+ * Find intervals.
+ */
+std::vector<Interval> findIntervals(const GeneOrder& go);
+
#endif
CPPUNIT_TEST_SUITE( TESTNAME );
CPPUNIT_TEST( testRobinsonSchensted );
CPPUNIT_TEST( testLongestSequences );
+ CPPUNIT_TEST( testFindIntervals );
+ CPPUNIT_TEST( testCountCycles );
CPPUNIT_TEST_SUITE_END();
protected:
GeneOrder go2(_validPerm2.begin(),_validPerm2.end());
p = longestSequences(go2);
- int first[] = {0,1,3,5,6,7,9};
- int second[] = {2,4,8};
CPPUNIT_ASSERT_EQUAL(7,p.first);
CPPUNIT_ASSERT_EQUAL(2,p.second);
}
+ void testFindIntervals (){
+ GeneOrder go(_validPerm.begin(),_validPerm.end());
+ vector<pair<size_t,size_t> > v = findIntervals(go);
+ CPPUNIT_ASSERT_EQUAL(4ul,v.size());
+ Interval go10(1,1);
+ Interval go12(3,3);
+ CPPUNIT_ASSERT(go10 == v[0]);
+ CPPUNIT_ASSERT(go12 == v[2]);
+
+ GeneOrder go2(_validPerm2.begin(),_validPerm2.end());
+ v = findIntervals(go);
+ CPPUNIT_ASSERT_EQUAL(9ul,v.size());
+ Interval go20(1,3);
+ Interval go22(1,4);
+ CPPUNIT_ASSERT(go20 == v[0]);
+ CPPUNIT_ASSERT(go22 == v[2]);
+ }
+ void testCountCycles (){
+ GeneOrder go(_validPerm.begin(),_validPerm.end());
+ int c = countCycles(go);
+ CPPUNIT_ASSERT_EQUAL(4,c);
+
+ GeneOrder go2(_validPerm3.begin(),_validPerm3.end());
+ c = countCycles(go2);
+ CPPUNIT_ASSERT_EQUAL(6,c);
+ }
};