From 79451fe868d3d11c0294383a2ddab95b40a0a4ce Mon Sep 17 00:00:00 2001
From: Michael Andreen <harv@ruin.nu>
Date: Sun, 24 Jun 2007 18:07:10 +0000
Subject: [PATCH] renamed a function and removed some debug output

---
 src/genesorter.cpp | 6 ++----
 src/genesorter.h   | 5 ++++-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/genesorter.cpp b/src/genesorter.cpp
index 03f19db..d73f176 100644
--- a/src/genesorter.cpp
+++ b/src/genesorter.cpp
@@ -35,7 +35,6 @@ GeneSorter::ActionList GeneSorter::sort(const GeneOrder& go){
 	ActionList al;
 	GeneOrder temp(go);
 	while(inversionDistance(temp) > 0){
-		cout << "AL: " << al.size() << " : ";
 		cout << "Distance: " << inversionDistance(temp) << " : ";
 		copy(temp.begin(), temp.end(), ostream_iterator<int>(cout, " "));
 		cout << endl;
@@ -43,7 +42,6 @@ GeneSorter::ActionList GeneSorter::sort(const GeneOrder& go){
 		if (safe.size() > 0){
 			safe[0](temp);
 			al.push_back(safe[0]);
-			cout << "AL: " << al.size() << " : ";
 		}else
 			return ActionList(); //TODO: Need to handle hurdles.
 	}
@@ -69,7 +67,7 @@ GeneSorter::ActionList GeneSorter::safeActions(const GeneOrder& go){
 	for (size_t i = 0; i < intervals.size(); ++i){
 		if (intervals[i].oriented && intervals[i].first != intervals[i].second){
 			SortAction sa(new ReverseAction(intervals[i]));
-			size_t score = scoreActions(go,sa);
+			size_t score = scoreAction(go,sa);
 			cout << "Inversion: " << min(intervals[i].first,intervals[i].second) << ":" << max(intervals[i].first,intervals[i].second)-1 << " Score: " << score <<  endl;
 			pq.push(pair<size_t,SortAction>(score,sa));
 		}				
@@ -81,7 +79,7 @@ GeneSorter::ActionList GeneSorter::safeActions(const GeneOrder& go){
 	return al;
 }
 
-size_t GeneSorter::scoreActions(const GeneOrder& go, SortAction& sa){
+size_t GeneSorter::scoreAction(const GeneOrder& go, SortAction& sa){
 	GeneOrder temp(go);
 	sa(temp);
 	vector<Interval> intervals = findIntervals(temp);
diff --git a/src/genesorter.h b/src/genesorter.h
index 4380e99..e06bedf 100644
--- a/src/genesorter.h
+++ b/src/genesorter.h
@@ -46,7 +46,10 @@ class GeneSorter{
 		 */
 		ActionList safeActions(const GeneOrder& go1);
 
-		size_t scoreActions(const GeneOrder& go, SortAction& sa);
+		/**
+		 * Calculates the score for an action given a gene order
+		 */
+		size_t scoreAction(const GeneOrder& go, SortAction& sa);
 
 		~GeneSorter(){};
 };
-- 
2.39.2