X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=tree.cpp;h=44ecadd534b60d60b602d9e052259ac69709f9d3;hp=ed652508ef2e6b049c183777ae5eecab42100d97;hb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;hpb=94d43af803e4be78b2ba8049669504e854ad13be

diff --git a/tree.cpp b/tree.cpp
index ed65250..44ecadd 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -588,18 +588,11 @@ int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
 	}
 }
 /*****************************************************************/
-void Tree::getCopy(Tree* copy, map<string, string> nameMap, vector<string> namesToInclude) {
+void Tree::getCopy(Tree* copy, map<string, string> nameMap) {
 	try {
         
 		//for each node in the tree copy its info
 		for (int i = 0; i < numNodes; i++) {
-			//copy name
-			tree[i].setName(copy->tree[i].getName());
-            
-			//copy group
-            vector<string> temp;
-			tree[i].setGroup(temp);
-			
 			//copy branch length
 			tree[i].setBranchLength(copy->tree[i].getBranchLength());
             
@@ -608,93 +601,9 @@ void Tree::getCopy(Tree* copy, map<string, string> nameMap, vector<string> names
             
 			//copy children
 			tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
-            
-			//copy index in node and tmap
-			tree[i].setIndex(copy->tree[i].getIndex());
-			setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
-			
-			//copy pGroups
-			tree[i].pGroups.clear();
-            
-			//copy pcount
-			tree[i].pcount.clear();
-		}
+        }
 		
-		groupNodeInfo.clear();
-        
-        //now lets change prune the seqs not in namesToInclude by setting their group to "doNotIncludeMe"
-        for (int i = 0; i < numLeaves; i++) {
-            
-            if (m->control_pressed) { break; }
-            
-			string name = tree[i].getName();
-            
-			map<string, string>::iterator itNames = nameMap.find(name);
-            
-			if (itNames == nameMap.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
-			else {
-				vector<string> dupNames;
-				m->splitAtComma(nameMap[name], dupNames);
-				
-				map<string, int>::iterator itCounts;
-				int maxPars = 1;
-				set<string> groupsAddedForThisNode;
-				for (int j = 0; j < dupNames.size(); j++) {
-					
-					string group = tmap->getGroup(dupNames[j]);
-                    bool includeMe = m->inUsersGroups(dupNames[j], namesToInclude);
-                    
-                    if (!includeMe && (group != "doNotIncludeMe")) { m->mothurOut("[ERROR] : creating subtree in copy.\n"); m->control_pressed = true; }
-					else if (!includeMe) {
-						if (groupsAddedForThisNode.count(group) == 0)  {  groupNodeInfo[group].push_back(i);  groupsAddedForThisNode.insert(group);  } //if you have not already added this node for this group, then add it
-						
-						//update pcounts
-						itCounts = tree[i].pcount.find(group);
-						if (itCounts == tree[i].pcount.end()) { //new group, add it
-							tree[i].pcount[group] = 1;
-						}else {
-							tree[i].pcount[group]++;
-						}
-                        
-						//update pgroups
-						itCounts = tree[i].pGroups.find(group);
-						if (itCounts == tree[i].pGroups.end()) { //new group, add it
-							tree[i].pGroups[group] = 1;
-						}else{
-							tree[i].pGroups[group]++;
-						}
-						
-						//keep highest group
-						if(tree[i].pGroups[group] > maxPars){
-							maxPars = tree[i].pGroups[group];
-						}
-                    }
-				}//end for
-				
-				if (maxPars > 1) { //then we have some more dominant groups
-					//erase all the groups that are less than maxPars because you found a more dominant group.
-					for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
-						if(it->second < maxPars){
-							tree[i].pGroups.erase(it++);
-						}else { it++; }
-					}
-					//set one remaining groups to 1
-					for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
-						tree[i].pGroups[it->first] = 1;
-					}
-				}//end if
-				
-				//update groups to reflect all the groups this node represents
-				vector<string> nodeGroups;
-				map<string, int>::iterator itGroups;
-				for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
-					nodeGroups.push_back(itGroups->first);
-				}
-				tree[i].setGroup(nodeGroups);
-				
-			}//end else
-		}//end for		
-        
+        if (nameMap.size() != 0) {  addNamesToCounts(nameMap);  }
         
         //build the pGroups in non leaf nodes to be used in the parsimony calcs.
 		for (int i = numLeaves; i < numNodes; i++) {