findIntervals implemented and passing test

[germs.git] / src / genealgorithms.cpp

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 154df354bc346592f53a1373b49bbc1c72a0b79d..eecdf3fea92bd8048c6c47fd1ef466d5e4698c67 100644 (file)
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -22,31 +22,16 @@
 #include "geneorder.h"
 
 #include <algorithm>
+#include <set>
 #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 +55,48 @@ std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go){
        }
        return v;
 }
+
+int countCycles(const GeneOrder& go){
+       int cycles = 0;
+       set<size_t> marked;
+       for (size_t p = 1; p < go.size() - 1; ++p){
+               if (marked.find(p) != marked.end())
+                       continue;
+       }
+       return cycles;
+}
+
+std::vector<Component> findComponents(const GeneOrder& go){
+       return vector<Component>();
+}
+
+//TODO: Think of a better than O(n^2) implementation
+std::vector<Interval> findIntervals(const GeneOrder& go){
+       vector<Interval> intervals;
+       for (size_t i = 0; i < go.size() - 1; ++i){
+               size_t f = 0;
+               size_t s = 0;
+               bool found = false;
+               size_t n = 0;
+               for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
+                       if (static_cast<size_t>(abs(*g)) == i){
+                               f = n;
+                               if (*g >= 0)
+                                       ++f;
+                               if (found)
+                                       break;
+                               found = true;
+                       }
+                       if(static_cast<size_t>(abs(*g)) == i+1){
+                               s = n;
+                               if (*g < 0)
+                                       ++s;
+                               if (found)
+                                       break;
+                               found = true;
+                       }
+               }
+               intervals.push_back(Interval(f,s));
+       }
+       return intervals;
+}