added permutation calculations to maximum-parsimony.cc

git-svn-id: svn://anubis/gvsu@303 45c1a28c-8058-47b2-ae61-ca45b979098e

cs677/pa4/maximum-parsimony.cc

@@ -11,6 +11,14 @@
 #include "PTree.h"
 using namespace std;
 
+static vector<Sequence *> sequences;
+static int num_seqs;
+
+void permute(int * array, int index);
+void usage();
+string getsequence(int fd);
+void evalPermutation(int * array);
+
 void usage()
 {
     cerr << "Usage: maximum-parsimony <sequence-file>" << endl;
@@ -77,7 +85,6 @@ int main(int argc, char * argv[])
         exit(1);
     }
 
-    vector<Sequence *> sequences;
     for (;;)
     {
         string seqstr = getsequence(fd);
@@ -89,12 +96,47 @@ int main(int argc, char * argv[])
 
     close(fd);
 
-    PTree tree(sequences);
-    cout << "tree:" << endl;
-    cout << tree;
-    cout << endl << "total count: " << tree.getCount() << endl;
+    num_seqs = sequences.size();
+    int indices[num_seqs];
+    for (int i = 0; i < num_seqs; i++)
+        indices[i] = 0;
+    permute(&indices[0], 0);
 
     MPI_Finalize();
 
     return 0;
 }
+
+void evalPermutation(int * array)
+{
+    for (int i = 0; i < num_seqs; i++)
+    {
+        cout << array[i] << "  ";
+    }
+    cout << endl;
+}
+
+void permute(int * array, int index)
+{
+    static int level = -1;
+    level++;
+    array[index] = level;
+
+    if (level == num_seqs)
+    {
+        evalPermutation(array);
+    }
+    else
+    {
+        for (int i = 0; i < num_seqs; i++)
+        {
+            if (array[i] == 0)
+            {
+                permute(array, i);
+            }
+        }
+    }
+
+    level--;
+    array[index] = 0;
+}