From a45ea752862a45a0868940280aeb837af270cf22 Mon Sep 17 00:00:00 2001
From: Michael Andreen <harv@ruin.nu>
Date: Wed, 29 Aug 2007 06:18:35 +0000
Subject: [PATCH] Added a Whirl model, which favors reversals, instead of using
 the standard

---
 src/model.cpp                    |  4 +++-
 src/modelidentifier.cpp          |  2 +-
 src/models.cpp                   | 11 +++++++++++
 src/models.h                     | 18 ++++++++++++++++++
 src/test/modelidentifiertest.cpp |  2 +-
 5 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/src/model.cpp b/src/model.cpp
index efd5c5f..f801f12 100644
--- a/src/model.cpp
+++ b/src/model.cpp
@@ -41,7 +41,9 @@ bool operator<(const Model& lh,const Model& rh){
 Model Model::modelFactory(const std::string& name){
 	if (name == "X"){
 		return Model(new Models::X());
-	}else if(name == "Whirl" || name == "Standard"){
+	}else if(name == "Whirl"){
+		return Model(new Models::Whirl());
+	}else if(name == "Standard"){
 		return Model(new Models::ModelImpl());
 	}else if(name == "Zipper"){
 		return Model(new Models::Zipper());
diff --git a/src/modelidentifier.cpp b/src/modelidentifier.cpp
index 820d75a..a7c67b8 100644
--- a/src/modelidentifier.cpp
+++ b/src/modelidentifier.cpp
@@ -83,7 +83,7 @@ priority_queue<pair<double,Model> > ModelIdentifier::identify(const GeneOrder& g
 	priority_queue<pair<double,Model> > scores;
 	scores.push(pair<double,Model>(output[0],Model(new Models::X)));
 	scores.push(pair<double,Model>(output[1],Model(new Models::Zipper)));
-	scores.push(pair<double,Model>(output[2],Model(new Models::ModelImpl)));
+	scores.push(pair<double,Model>(output[2],Model(new Models::Whirl)));
 	scores.push(pair<double,Model>(output[3],Model(new Models::FatX)));
 	scores.push(pair<double,Model>(output[4],Model(new Models::Cloud)));
 	return scores;
diff --git a/src/models.cpp b/src/models.cpp
index a8289c7..0511dd4 100644
--- a/src/models.cpp
+++ b/src/models.cpp
@@ -36,6 +36,17 @@ const char* ModelImpl::name(){
 }
 
 
+double Whirl::score(const SortAction& sa, const GeneOrder& go){
+	const ReverseAction* ra = dynamic_cast<const ReverseAction*>(&sa.impl());
+
+	if (ra){
+		return 1;
+	}
+	return -1;
+}
+const char* Whirl::name(){
+	return "Whirl";
+}
 
 double X::score(const SortAction& sa, const GeneOrder& go){
 	const ReverseAction* ra = dynamic_cast<const ReverseAction*>(&sa.impl());
diff --git a/src/models.h b/src/models.h
index f037071..c1c96d1 100644
--- a/src/models.h
+++ b/src/models.h
@@ -46,6 +46,24 @@ class ModelImpl {
 		virtual const char* name();
 };
 
+/**
+ * A model that favors reversals.
+ */
+class Whirl : public ModelImpl {
+	public:
+		/**
+		 * Returns a higher score for reversals and a lower score
+		 * for all other actions.
+		 *
+		 * \see Model::score
+		 */
+		double score(const SortAction& sa, const GeneOrder& go);
+
+		/**
+		 * \see Model::name
+		 */
+		const char* name();
+};
 
 /**
  * A model that favors symmetric reversal, resulting in an X-like
diff --git a/src/test/modelidentifiertest.cpp b/src/test/modelidentifiertest.cpp
index 7a0cedd..b4848cc 100644
--- a/src/test/modelidentifiertest.cpp
+++ b/src/test/modelidentifiertest.cpp
@@ -67,7 +67,7 @@ protected:
 
 		GeneOrder uniform(_uniform.begin(),_uniform.end());
 		pq = mi.identify(uniform);
-		CPPUNIT_ASSERT_EQUAL(string("Standard"),string(pq.top().second.name()));
+		CPPUNIT_ASSERT_EQUAL(string("Whirl"),string(pq.top().second.name()));
 
 		GeneOrder zipper(_zipper.begin(),_zipper.end());
 		pq = mi.identify(zipper);
-- 
2.39.2