From 6724d50f2d36dccd383d95d36f7fe328b2692bc0 Mon Sep 17 00:00:00 2001
From: Michael Andreen <harv@ruin.nu>
Date: Tue, 19 Jun 2007 10:36:11 +0000
Subject: [PATCH] countCycles implemented and passess test

---
 src/genealgorithms.cpp          | 6 ++----
 src/test/genealgorithmstest.cpp | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index ec3a92e..d9d86a3 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -68,7 +68,6 @@ struct FindP{
 std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
 	vector<Interval> points;
 	for (size_t p = 1; p <= intervals.size(); ++p){
-		cout << endl << "Point " << p << " : ";
 		size_t f = 0;
 		size_t s = 0;
 		bool found = false;
@@ -93,7 +92,6 @@ std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
 				}
 			}
 		}
-		cout << f << ":" << s << endl;
 		points.push_back(Interval(f,s));
 	}
 	return points;
@@ -104,12 +102,12 @@ int countCycles(const GeneOrder& go){
 	int cycles = 0;
 	set<size_t> marked;
 	vector<Interval> intervals = findIntervals(go);
-	vector<Interval> points;
+	vector<Interval> points = findIntervalsAtPoints(intervals);
 	for (size_t p = 1; p < go.size(); ++p){
 		if (marked.find(p) != marked.end())
 			continue;
 		Interval i = intervals[points[p-1].first];
-		while (marked.find(p) != marked.end()){
+		while (marked.find(p) == marked.end()){
 			marked.insert(p);
 			if (i == intervals[points[p-1].first])
 				i = intervals[points[p-1].second];
diff --git a/src/test/genealgorithmstest.cpp b/src/test/genealgorithmstest.cpp
index 0fca4d2..3f57e0f 100644
--- a/src/test/genealgorithmstest.cpp
+++ b/src/test/genealgorithmstest.cpp
@@ -24,7 +24,7 @@ class TESTNAME : public CPPUNIT_NS::TestFixture
   CPPUNIT_TEST( testLongestSequences );
   CPPUNIT_TEST( testFindIntervals );
   CPPUNIT_TEST( testFindIntervalsAtPoints );
-  //CPPUNIT_TEST( testCountCycles );
+  CPPUNIT_TEST( testCountCycles );
   CPPUNIT_TEST_SUITE_END();
 
 protected:
-- 
2.39.2