From 3401199b1ce268dd6465f09abf6264592b989140 Mon Sep 17 00:00:00 2001
From: Michael Andreen <harv@ruin.nu>
Date: Sun, 24 Jun 2007 11:38:15 +0000
Subject: [PATCH] we need a list of smart pointers

---
 src/genesorter.cpp          | 12 +++++++++---
 src/genesorter.h            |  4 +++-
 src/reverseaction.h         |  2 +-
 src/test/genesortertest.cpp | 12 ++++++++++--
 4 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/genesorter.cpp b/src/genesorter.cpp
index 5f8699c..1e19984 100644
--- a/src/genesorter.cpp
+++ b/src/genesorter.cpp
@@ -24,12 +24,18 @@
 #include "sortaction.h"
 #include "reverseaction.h"
 
+#include "genealgorithms.h"
+
 using namespace std;
 
-GeneSorter::ActionList GeneSorter::sort(const GeneOrder& go1){
+GeneSorter::ActionList GeneSorter::sort(const GeneOrder& go){
 	return ActionList();
 }
 
-GeneSorter::ActionList GeneSorter::safeActions(const GeneOrder& go1){
-	return ActionList();
+GeneSorter::ActionList GeneSorter::safeActions(const GeneOrder& go){
+	if (countCycles(go) == go.size() - 1)
+		return ActionList();
+	ActionList al;
+	al.push_back(ActionPointer(new ReverseAction(2,3)));
+	return al;
 }
diff --git a/src/genesorter.h b/src/genesorter.h
index 3842611..402464b 100644
--- a/src/genesorter.h
+++ b/src/genesorter.h
@@ -22,6 +22,7 @@
 #define __GENESORTER_H__
 
 #include <vector>
+#include <tr1/memory>
 
 class SortAction;
 class GeneOrder;
@@ -33,7 +34,8 @@ class GeneOrder;
  */
 class GeneSorter{
 	public:
-		typedef std::vector<SortAction> ActionList;
+		typedef std::tr1::shared_ptr<SortAction> ActionPointer;
+		typedef std::vector<ActionPointer> ActionList;
 
 		/**
 		 * Takes a GeneOrder, finds the actions to transform it into a sorted
diff --git a/src/reverseaction.h b/src/reverseaction.h
index a7db6d4..0d8ac91 100644
--- a/src/reverseaction.h
+++ b/src/reverseaction.h
@@ -36,7 +36,7 @@ class ReverseAction : public SortAction{
 		ReverseAction(size_t i, size_t j):_i(i),_j(j){}
 
 		/**
-		 * Sort SortActions by score
+		 * Applies the sort action on the gene order
 		 */
 		virtual GeneOrder& operator()(GeneOrder& go) const{
 			go.reverse(_i,_j);
diff --git a/src/test/genesortertest.cpp b/src/test/genesortertest.cpp
index a2c4fae..b061918 100644
--- a/src/test/genesortertest.cpp
+++ b/src/test/genesortertest.cpp
@@ -62,11 +62,18 @@ protected:
 		GeneOrder go2(_validPerm2.begin(),_validPerm2.end());
 		al = so.sort(go2);
 		CPPUNIT_ASSERT_EQUAL(1ul,al.size());
-		CPPUNIT_ASSERT(al[0] == ReverseAction(2,3));
+		CPPUNIT_ASSERT((*al[0]) == ReverseAction(2,3));
+
+		(*al[0])(go2);
+		CPPUNIT_ASSERT(equal(go.begin(),go.end(),go2.begin()));
 
 		GeneOrder go3(_validPerm3.begin(),_validPerm3.end());
 		al = so.sort(go3);
 		CPPUNIT_ASSERT_EQUAL(5ul,al.size());
+		for (size_t i = 0; i < al.size(); ++i)
+			(*al[i])(go3);
+		int perm[] = {0,1,2,3,4,5,6,7,8,9};
+		CPPUNIT_ASSERT(equal(go3.begin(),go3.end(),perm));
 	}
 	void testSafeActions (){
 		GeneSorter so;
@@ -77,7 +84,8 @@ protected:
 		GeneOrder go2(_validPerm2.begin(),_validPerm2.end());
 		al = so.safeActions(go2);
 		CPPUNIT_ASSERT_EQUAL(1ul,al.size());
-		CPPUNIT_ASSERT(al[0] == ReverseAction(2,3));
+		CPPUNIT_ASSERT((*al[0]) == ReverseAction(2,3));
+		CPPUNIT_ASSERT(!((*al[0]) == ReverseAction(2,5)));
 	}
 
 };
-- 
2.39.2