findComponents implemented and passes test

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index e96c9be63e9d378187a0d58b9413905bf6517e20..a32968eaea3454f1081649335a34c7e8c201077f 100644 (file)
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -23,6 +23,7 @@
 
 #include <algorithm>
 #include <set>
+#include <stack>
 #include <cstdlib>
 #include <iostream>
 using namespace std;
@@ -91,8 +92,80 @@ int countCycles(const GeneOrder& go){
        return cycles;
 }
 
+int sign(Gene g){
+       if (g > 0)
+               return 1;
+       if (g < 0)
+               return -1;
+       return 0;
+}
+
+struct Abs{
+       Gene operator()(Gene x) const{
+               return abs(x);
+       }
+};
 std::vector<Component> findComponents(const GeneOrder& go){
-       return vector<Component>();
+       vector<Component> components;
+       vector<int> os(go.size()-1);
+       for (size_t i = 0; i < os.size(); ++i)
+               os[i] = (go[i]*go[i+1] > 0 ? sign(go[i]) : 0);
+       stack<Gene> Mdir;
+       Mdir.push(go.size()-1);
+       stack<Gene> Mrev;
+       Mrev.push(0);
+       stack<size_t> Sdir;
+       Sdir.push(0);
+       stack<size_t> Srev;
+       Srev.push(0);
+       vector<Gene> dir;
+       dir.push_back(go.size()-1);
+       vector<Gene> rev;
+       rev.push_back(0);
+       size_t s;
+       vector<Gene> p(go.list());
+       transform(p.begin(),p.end(),p.begin(),Abs());
+       for (size_t i = 1; i < go.size(); ++i){
+               //Directed
+               if (p[i-1] > p[i])
+                       Mdir.push(p[i-1]);
+               else while (Mdir.top() < p[i])
+                       Mdir.pop();
+               dir.push_back(Mdir.top());
+
+               s = Sdir.top();
+               while(p[Sdir.top()] > p[i] || dir[Sdir.top()] < p[i]){
+                       Sdir.pop();
+                       os[Sdir.top()] = (os[Sdir.top()] == os[s] ? os[s] : 0);
+                       s = Sdir.top();
+               }
+               if (go[i] > 0 && dir[i] == dir[s] && i - s == p[i] - p[s])
+                       components.push_back(Component(p[s],p[i],(s+1 == i ? 0 : os[s])));
+
+
+               //Reverse
+               if (p[i-1] < p[i])
+                       Mrev.push(p[i-1]);
+               else while (Mrev.top() > p[i])
+                       Mrev.pop();
+               rev.push_back(Mrev.top());
+
+               s = Srev.top();
+               while((p[s] < p[i] || rev[s] > p[i]) && s > 0){
+                       Srev.pop();
+                       os[Srev.top()] *= (os[Srev.top()] == os[s] ? 1 : 0);
+                       s = Srev.top();
+               }
+               if (go[i] < 0 && rev[i] == rev[s] && i - s == p[s] - p[i])
+                       components.push_back(Component(-p[s],-p[i],os[s]));
+
+               //Update stacks
+               if (go[i] > 0)
+                       Sdir.push(i);
+               else
+                       Srev.push(i);
+       }
+       return components;
 }
 
 /**

diff --git a/src/genealgorithms.h b/src/genealgorithms.h
index b0e75b9f65790e184eabe46b6bf9ec9dba8d1002..0158c35108616b4fd18b452ec357fa39841005c3 100644 (file)
--- a/src/genealgorithms.h
+++ b/src/genealgorithms.h
@@ -27,6 +27,9 @@ class GeneOrder;
 
 struct Component{
        Component(int b,int e,int s):begin(b),end(e),sign(s){}
+       bool operator==(const Component& c){
+               return begin == c.begin && end == c.end && sign == c.sign;
+       }
        int begin;
        int end;
        int sign;

diff --git a/src/test/genealgorithmstest.cpp b/src/test/genealgorithmstest.cpp
index 1d7f2d04e2a2d3597d4fb78e8de3815302257466..f2bd11898b5a5a846d4364bc6073d903265d103c 100644 (file)
--- a/src/test/genealgorithmstest.cpp
+++ b/src/test/genealgorithmstest.cpp
@@ -25,6 +25,7 @@ class TESTNAME : public CPPUNIT_NS::TestFixture
   CPPUNIT_TEST( testFindIntervals );
   CPPUNIT_TEST( testFindIntervalsAtPoints );
   CPPUNIT_TEST( testCountCycles );
+  CPPUNIT_TEST( testFindComponents );
   CPPUNIT_TEST_SUITE_END();
 
 protected:
@@ -128,6 +129,36 @@ protected:
                CPPUNIT_ASSERT_EQUAL(6,c);
        }
 
+       void testFindComponents (){
+               GeneOrder go(_validPerm.begin(),_validPerm.end());
+               vector<Component> v = findComponents(go);
+               CPPUNIT_ASSERT_EQUAL(4ul,v.size());
+               Component go10(0,1,0);
+               Component go11(1,2,0);
+               Component go12(2,3,0);
+               Component go13(3,4,0);
+               CPPUNIT_ASSERT(go10 == v[0]);
+               CPPUNIT_ASSERT(go11 == v[1]);
+               CPPUNIT_ASSERT(go12 == v[2]);
+               CPPUNIT_ASSERT(go13 == v[3]);
+               
+               GeneOrder go2(_validPerm3.begin(),_validPerm3.end());
+               v = findComponents(go2);
+               CPPUNIT_ASSERT_EQUAL(6ul,v.size());
+               Component go20(1,2,0);
+               Component go21(0,4,0);
+               Component go22(4,7,1);
+               Component go23(-15,-12,-1);
+               Component go24(-12,-9,-1);
+               Component go25(7,16,0);
+               CPPUNIT_ASSERT(go20 == v[0]);
+               CPPUNIT_ASSERT(go21 == v[1]);
+               CPPUNIT_ASSERT(go22 == v[2]);
+               CPPUNIT_ASSERT(go23 == v[3]);
+               CPPUNIT_ASSERT(go24 == v[4]);
+               CPPUNIT_ASSERT(go25 == v[5]);
+       }
+
 };
 
 CPPUNIT_TEST_SUITE_REGISTRATION( TESTNAME );