X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=174c6f7b0414277b006b562f2736a83077db9fb7;hb=6ba92ada02bfbb04abb8a0c7a039ec63c7c9921e;hp=67c504e77b3f9bdfad9589236e8f65f8e2b2cd5d;hpb=e44303f027e957d05c9e9418fbd68171f3707599;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 67c504e..174c6f7 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -20,6 +20,7 @@
 
 #include "genealgorithms.h"
 #include "geneorder.h"
+#include "componenttree.h"
 
 #include <algorithm>
 #include <set>
@@ -146,7 +147,7 @@ std::vector<Component> findComponents(const GeneOrder& go){
 			s = Sdir.top();
 		}
 		if (go[i] > 0 && dir[i] == dir[s] && static_cast<Gene>(i - s) == p[i] - p[s])
-			components.push_back(Component(p[s],p[i],(s+1 == i ? 0 : os[s])));
+			components.push_back(Component(p[s],p[i],(s+1 == i ? 0 : os[s]),s,i));
 
 		//Reverse
 		if (p[i-1] < p[i])
@@ -162,7 +163,7 @@ std::vector<Component> findComponents(const GeneOrder& go){
 			s = Srev.top();
 		}
 		if (go[i] < 0 && rev[i] == rev[s] && static_cast<Gene>(i - s) == p[s] - p[i])
-			components.push_back(Component(-p[s],-p[i],(s+1 == i ? 0 : os[s])));
+			components.push_back(Component(-p[s],-p[i],(s+1 == i ? 0 : os[s]),s,i));
 
 		//Update stacks
 		if (go[i] > 0)
@@ -173,18 +174,40 @@ std::vector<Component> findComponents(const GeneOrder& go){
 	return components;
 }
 
+int sign2(Gene g){
+	if (g < 0)
+		return -1;
+	return 1;
+}
 /**
  * 
  */
 std::vector<Interval> findIntervals(const GeneOrder& go){
-	vector<Interval> intervals(go.size()-1,Interval(go.size(),go.size()));
+	const size_t max = go.size();
+	vector<Interval> intervals(go.size()-1,Interval(max,max,false));
 	size_t n = 0;
-	for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
+	const GeneOrder::iterator end = go.end();
+	for (GeneOrder::iterator g = go.begin(); g != end; ++g, ++n){
 			size_t i = abs(*g);
-			if (i < go.size() - 1)
-				intervals[i].first = n + (*g >= 0 ? 1 : 0);
-			if (i > 0)
-				intervals[i-1].second = n + (*g < 0 ? 1 : 0);
+			if (i < max - 1){
+				Interval& curr = intervals[i];
+				curr.first = n + (*g >= 0 ? 1 : 0);
+
+				if (curr.second == max)
+					curr.oriented = *g < 0;
+				else
+					curr.oriented ^=  *g < 0;
+			}
+			if (i > 0){
+				Interval& prev = intervals[i-1];
+				prev.second = n + (*g < 0 ? 1 : 0);
+
+				if (prev.first == max)
+					prev.oriented = *g < 0;
+				else
+					prev.oriented ^=  *g < 0;
+			}
+
 	}
 	return intervals;
 }
@@ -194,7 +217,7 @@ std::vector<Interval> findIntervals(const GeneOrder& go){
  */
 std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
 	size_t max = intervals.size()+1;
-	vector<Interval> points(max,Interval(max,max));
+	vector<Interval> points(max,Interval(max,max,false));
 	size_t n = 0;
 	for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
 		if (points[i->first].first == max){