worked on unifrac.unweighted()

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 5029438b6e632e0274f88dca33ba121ec238bf26..642c6658739dd5252b2d61083ce6af2b872785ec 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -303,12 +303,9 @@ map<string,int> Tree::mergeGcounts(int position) {
 }
 /**************************************************************************************************/
 
-void Tree::randomLabels() {
+void Tree::randomLabels(vector<string> g) {
        try {
                
-               //set up the groups the user wants to include
-               setGroups();
-               
                for(int i = 0; i < numLeaves; i++){
                        int z;
                        //get random index to switch with
@@ -318,8 +315,8 @@ void Tree::randomLabels() {
                        //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;
                
-                       treez = inUsersGroups(tree[z].getGroup(), globaldata->Groups);
-                       treei = inUsersGroups(tree[i].getGroup(), globaldata->Groups);
+                       treez = inUsersGroups(tree[z].getGroup(), g);
+                       treei = inUsersGroups(tree[i].getGroup(), g);
                        
                        if ((treez == true) && (treei == true)) {
                                //switches node i and node z's info.
@@ -405,8 +402,8 @@ void Tree::randomBlengths()  {
        }               
 }
 /*************************************************************************************************/
-void Tree::assembleRandomUnifracTree() {
-       randomLabels();
+void Tree::assembleRandomUnifracTree(vector<string> g) {
+       randomLabels(g);
        assembleTree();
 }
 /*************************************************************************************************/
@@ -538,46 +535,6 @@ void Tree::printBranch(int node) {
 
 /*****************************************************************/
 
-void Tree::setGroups() {
-       try {
-               //if the user has not entered specific groups to analyze then do them all
-               if (globaldata->Groups.size() != 0) {
-                       //check that groups are valid
-                       for (int i = 0; i < globaldata->Groups.size(); i++) {
-                               if (globaldata->gTreemap->isValidGroup(globaldata->Groups[i]) != true) {
-                                       cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
-                                       // erase the invalid group from globaldata->Groups
-                                       globaldata->Groups.erase (globaldata->Groups.begin()+i);
-                               }
-                       }
-                       
-                       //if the user only entered invalid groups
-                       if (globaldata->Groups.size() == 0) { 
-                               cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl; 
-                               for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
-                                       globaldata->Groups.push_back(globaldata->gTreemap->namesOfGroups[i]);
-                               }
-                       }
-                                       
-               }else {
-                       for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
-                               globaldata->Groups.push_back(globaldata->gTreemap->namesOfGroups[i]);
-                       }
-               }
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the Tree class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
-
-}
-
-/*****************************************************************/
-
 void Tree::printTree() {
        
        for(int i=0;i<numNodes;i++){