From: Michael Andreen <harv@ruin.nu>
Date: Wed, 20 Jun 2007 09:08:42 +0000 (+0000)
Subject: findComponents implemented and passes test
X-Git-Tag: v0.1~57
X-Git-Url: https://ruin.nu/git/?p=germs.git;a=commitdiff_plain;h=052ccbc26078638efee3614cd7cc2ea485313cad

findComponents implemented and passes test
---

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index e96c9be..a32968e 100644
--- 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 b0e75b9..0158c35 100644
--- 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 1d7f2d0..f2bd118 100644
--- 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 );