X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=174c6f7b0414277b006b562f2736a83077db9fb7;hb=dcd966c5fca7dca53ca1f605f70f13f019d29771;hp=e96c9be63e9d378187a0d58b9413905bf6517e20;hpb=bd6d14a70222d80caf00cee73b3014d392dbc69f;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index e96c9be..174c6f7 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -20,9 +20,11 @@
 
 #include "genealgorithms.h"
 #include "geneorder.h"
+#include "componenttree.h"
 
 #include <algorithm>
 #include <set>
+#include <stack>
 #include <cstdlib>
 #include <iostream>
 using namespace std;
@@ -65,8 +67,8 @@ struct FindP{
 };
 
 
-int countCycles(const GeneOrder& go){
-	int cycles = 0;
+size_t countCycles(const GeneOrder& go){
+	size_t cycles = 0;
 	set<size_t> marked;
 	vector<Interval> intervals = findIntervals(go);
 	vector<Interval> points = findIntervalsAtPoints(intervals);
@@ -91,22 +93,121 @@ int countCycles(const GeneOrder& go){
 	return cycles;
 }
 
+size_t inversionDistance(const GeneOrder& go){
+	size_t cycles = countCycles(go);
+
+	return go.size() - 1 - cycles;
+}
+
+int sign(Gene g){
+	if (g > 0)
+		return 1;
+	if (g < 0)
+		return -1;
+	return 0;
+}
+
+struct Abs{
+	Gene operator()(Gene x) const{
+		return abs(x);
+	}
+};
 std::vector<Component> findComponents(const GeneOrder& go){
-	return vector<Component>();
+	vector<Component> components;
+	vector<int> os(go.size()-1);
+	for (size_t i = 0; i < os.size(); ++i)
+		os[i] = (go[i]*go[i+1] > 0 ? sign(go[i]) : 0);
+	stack<Gene> Mdir;
+	Mdir.push(go.size()-1);
+	stack<Gene> Mrev;
+	Mrev.push(0);
+	stack<size_t> Sdir;
+	Sdir.push(0);
+	stack<size_t> Srev;
+	Srev.push(0);
+	vector<Gene> dir;
+	dir.push_back(go.size()-1);
+	vector<Gene> rev;
+	rev.push_back(0);
+	size_t s;
+	vector<Gene> p(go.list());
+	transform(p.begin(),p.end(),p.begin(),Abs());
+	for (size_t i = 1; i < go.size(); ++i){
+		//Directed
+		if (p[i-1] > p[i])
+			Mdir.push(p[i-1]);
+		else while (Mdir.top() < p[i])
+			Mdir.pop();
+		dir.push_back(Mdir.top());
+
+		s = Sdir.top();
+		while(p[Sdir.top()] > p[i] || dir[Sdir.top()] < p[i]){
+			Sdir.pop();
+			os[Sdir.top()] = (os[Sdir.top()] == os[s] ? os[s] : 0);
+			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]),s,i));
+
+		//Reverse
+		if (p[i-1] < p[i])
+			Mrev.push(p[i-1]);
+		else while (Mrev.top() > p[i])
+			Mrev.pop();
+		rev.push_back(Mrev.top());
+
+		s = Srev.top();
+		while((p[s] < p[i] || rev[s] > p[i]) && s > 0){
+			Srev.pop();
+			os[Srev.top()] *= (os[Srev.top()] == os[s] ? 1 : 0);
+			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]),s,i));
+
+		//Update stacks
+		if (go[i] > 0)
+			Sdir.push(i);
+		else
+			Srev.push(i);
+	}
+	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;
 }
@@ -116,7 +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){