fixed unweighted calculator

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 94ab326d8f6ba32ededf4f5b2240dc5852e4816c..2ad46f044f71556a9726c93a96d4fcd5ae42a6b6 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -231,33 +231,51 @@ map<string,int> Tree::mergeGcounts(int position) {
 
 void Tree::randomLabels() {
        try {
+               
+               //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;
                        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;
                                }
                        }
+                       
+                       //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);
+                       
+                       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);
                
-                       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);
-               
-                       map<string,int> gcount_hold = tree[z].pcount;
-                       tree[z].pcount = (tree[i].pcount);
-                       tree[i].pcount = (gcount_hold);
+                               map<string,int> gcount_hold = tree[z].pcount;
+                               tree[z].pcount = (tree[i].pcount);
+                               tree[i].pcount = (gcount_hold);
+                       }
                }
        }
        catch(exception& e) {
@@ -416,6 +434,41 @@ 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);
+       }               
 
-
+}