a little cleanup and minor fix

[germs.git] / src / genealgorithms.cpp

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 154df354bc346592f53a1373b49bbc1c72a0b79d..78b0f0572dc283b1e7e8f7278303954ff77cddac 100644 (file)
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -22,31 +22,17 @@
 #include "geneorder.h"
 
 #include <algorithm>
+#include <set>
+#include <stack>
 #include <cstdlib>
+#include <iostream>
 using namespace std;
 
 std::pair<int,int> longestSequences(const GeneOrder& go){
+       vector<vector<int> > v = robinsonSchensted(go);
+       return pair<int,int>(v[0].size(),v.size());
 }
 
-
-/*
-robSche2 :: [Int] -> [[Int]] -> [[Int]]
-robSche2 [] ys = ys
-robSche2 (x:xs) ys = robSche2 xs $ robSche4 x ys
-
-robSche3 :: Int -> [Int] -> (Maybe Int,[Int])
-robSche3 x ys = let yless = [y | y <- ys, y < x] in
-       let ymore = [y | y <- ys, y > x] in
-               case ymore of
-                       [] -> (Nothing, yless++[x])
-                       (y:ys) -> (Just y, yless++(x:ys))
-
-robSche4 :: Int -> [[Int]] -> [[Int]]
-robSche4 x [] = [[x]]
-robSche4 x (y:ys) = case robSche3 x y of
-       (Nothing, y) -> y:ys
-       (Just x, y) -> y:robSche4 x ys
-*/
 std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go){
        vector<vector<int> > v;
        for (GeneOrder::iterator i = go.begin(); i != go.end(); ++i){
@@ -70,3 +56,151 @@ std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go){
        }
        return v;
 }
+
+struct FindP{
+       size_t p;
+       FindP(size_t p) : p(p) {}
+       bool operator()(Interval i){
+               return (i.first == p || i.second == p);
+       }
+};
+
+
+int countCycles(const GeneOrder& go){
+       int cycles = 0;
+       set<size_t> marked;
+       vector<Interval> intervals = findIntervals(go);
+       vector<Interval> points = findIntervalsAtPoints(intervals);
+       for (size_t p = 1; p < go.size(); ++p){
+               if (marked.find(p) != marked.end())
+                       continue;
+               Interval i = intervals[points[p].first];
+               while (marked.find(p) == marked.end()){
+                       marked.insert(p);
+                       if (i == intervals[points[p].first])
+                               i = intervals[points[p].second];
+                       else
+                               i = intervals[points[p].first];
+
+                       if (p == i.first)
+                               p = i.second;
+                       else
+                               p = i.first;
+               }
+               ++cycles;
+       }
+       return 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){
+       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])));
+
+               //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])));
+
+               //Update stacks
+               if (go[i] > 0)
+                       Sdir.push(i);
+               else
+                       Srev.push(i);
+       }
+       return components;
+}
+
+/**
+ * 
+ */
+std::vector<Interval> findIntervals(const GeneOrder& go){
+       vector<Interval> intervals(go.size()-1,Interval(go.size(),go.size()));
+       size_t n = 0;
+       for (GeneOrder::iterator g = go.begin(); g != go.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);
+       }
+       return intervals;
+}
+
+/**
+ * 
+ */
+std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
+       size_t max = intervals.size()+1;
+       vector<Interval> points(max,Interval(max,max));
+       size_t n = 0;
+       for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
+               if (points[i->first].first == max){
+                       points[i->first].first = n;
+               }else
+                       points[i->first].second = n;
+                       
+               if (points[i->second].first == max){
+                       points[i->second].first = n;
+               }else
+                       points[i->second].second = n;
+       }
+       return points;
+
+}