weightedcommand

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index eea3af4dea1f5db04cb689b052fb0177ef03e7f3..2689b037f6a494474ce1e008ba5efb1d250f0791 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -309,43 +309,32 @@ void Tree::randomLabels() {
                //set up the groups the user wants to include
                setGroups();
                
-               for(int i=numLeaves-1;i>=0;i--){
-                       if(tree[i].pGroups.size() == 0){
-                               continue;
-                       }
-                       
-                       int escape = 1;
+               for(int i = 0; i < numLeaves; i++){
                        int z;
-               
-                       while(escape == 1){
-                               //get random index to switch with
-                               z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));        
-                       
-                               if(tree[z].pGroups.size() != 0){
-                                       escape = 0;
-                               }
-                       }
+                       //get random index to switch with
+                       z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));        
                        
                        //you only want to randomize the nodes that are from a group the user wants analyzed, so
                        //if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
                        bool treez, treei;
-                       
-                       //leaves have only one group so you can just set it to begin()
-                       it = tree[z].pGroups.begin();
-                       treez = inUsersGroups(it->first, globaldata->Groups);
-                       
-                       it = tree[i].pGroups.begin();
-                       treei = inUsersGroups(it->first, globaldata->Groups);
+               
+                       treez = inUsersGroups(tree[z].getGroup(), globaldata->Groups);
+                       treei = inUsersGroups(tree[i].getGroup(), globaldata->Groups);
                        
                        if ((treez == true) && (treei == true)) {
                                //switches node i and node z's info.
                                map<string,int> lib_hold = tree[z].pGroups;
                                tree[z].pGroups = (tree[i].pGroups);
                                tree[i].pGroups = (lib_hold);
-               
-                               tree[z].setGroup(tree[z].pGroups.begin()->first);
-                               tree[i].setGroup(tree[i].pGroups.begin()->first);
-               
+                               
+                               string zgroup = tree[z].getGroup();
+                               tree[z].setGroup(tree[i].getGroup());
+                               tree[i].setGroup(zgroup);
+                               
+                               string zname = tree[z].getName();
+                               tree[z].setName(tree[i].getName());
+                               tree[i].setName(zname);
+                               
                                map<string,int> gcount_hold = tree[z].pcount;
                                tree[z].pcount = (tree[i].pcount);
                                tree[i].pcount = (gcount_hold);
@@ -363,6 +352,45 @@ void Tree::randomLabels() {
 }
 /**************************************************************************************************/
 
+void Tree::randomLabels(string groupA, string groupB) {
+       try {
+               for(int i = 0; i < numLeaves; i++) {
+                       int z;
+                       //get random index to switch with
+                       z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));        
+                       
+                       //you only want to randomize the nodes that are from a group the user wants analyzed, so
+                       //if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
+                       if (((tree[z].getGroup() == groupA) || (tree[z].getGroup() == groupB)) && ((tree[i].getGroup() == groupA) || (tree[i].getGroup() == groupB))) {
+                               //switches node i and node z's info.
+                               map<string,int> lib_hold = tree[z].pGroups;
+                               tree[z].pGroups = (tree[i].pGroups);
+                               tree[i].pGroups = (lib_hold);
+                               
+                               string zgroup = tree[z].getGroup();
+                               tree[z].setGroup(tree[i].getGroup());
+                               tree[i].setGroup(zgroup);
+                               
+                               string zname = tree[z].getName();
+                               tree[z].setName(tree[i].getName());
+                               tree[i].setName(zname);
+                               
+                               map<string,int> gcount_hold = tree[z].pcount;
+                               tree[z].pcount = (tree[i].pcount);
+                               tree[i].pcount = (gcount_hold);
+                       }
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
+/**************************************************************************************************/
 void Tree::randomBlengths()  {
        try {
                for(int i=numNodes-1;i>=0;i--){
@@ -387,6 +415,11 @@ void Tree::assembleRandomUnifracTree() {
        randomLabels();
        assembleTree();
 }
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
+       randomLabels(groupA, groupB);
+       assembleTree();
+}
 
 /*************************************************************************************************/
 //for now it's just random topology but may become random labels as well later that why this is such a simple function now...
@@ -439,16 +472,18 @@ void Tree::randomTopology() {
 
 /*****************************************************************/
 // This prints out the tree in Newick form.
-void Tree::createNewickFile() {
+void Tree::createNewickFile(string f) {
        try {
                int root = findRoot();
-               filename = getRootName(globaldata->getTreeFile()) + "newick";
+               //filename = getRootName(globaldata->getTreeFile()) + "newick";
+               filename = f;
                openOutputFile(filename, out);
                
                printBranch(root);
                
                // you are at the end of the tree
                out << ";" << endl;
+               out.close();
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -493,7 +528,7 @@ void Tree::printBranch(int node) {
                        printBranch(tree[node].getRChild());
                        out << ")";
                }else { //you are a leaf
-                       tree[node].printNode();  //prints out name and branch length
+                       out << tree[node].getName() << ":" << tree[node].getBranchLength();
                }
                
        }