X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=44ecadd534b60d60b602d9e052259ac69709f9d3;hb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;hp=7c9671bf9a91e02b23cfd40b44804c38e3e4354d;hpb=f55cf350ca6643f8eb070d8336e1957699a3f109;p=mothur.git

diff --git a/tree.cpp b/tree.cpp
index 7c9671b..44ecadd 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -92,7 +92,6 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
 		m = MothurOut::getInstance();
 		
 		if (m->runParse == true) {  parseTreeFile();  m->runParse = false;  }
-        //for(int i = 0; i < 	globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }	
 		numLeaves = m->Treenames.size();
 		numNodes = 2*numLeaves - 1;
 		
@@ -134,12 +133,11 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
         //build tree from matrix
         //initialize indexes
         map<int, int> indexes;  //maps row in simMatrix to vector index in the tree
-        int numGroups = (tmap->getNamesOfGroups()).size();
-        for (int g = 0; g < numGroups; g++) {	indexes[g] = g;	}
+        for (int g = 0; g < numLeaves; g++) {	indexes[g] = g;	}
 		
 		//do merges and create tree structure by setting parents and children
 		//there are numGroups - 1 merges to do
-		for (int i = 0; i < (numGroups - 1); i++) {
+		for (int i = 0; i < (numLeaves - 1); i++) {
 			float largest = -1000.0;
 			
 			if (m->control_pressed) { break; }
@@ -154,11 +152,11 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
             
 			//set non-leaf node info and update leaves to know their parents
 			//non-leaf
-			tree[numGroups + i].setChildren(indexes[row], indexes[column]);
+			tree[numLeaves + i].setChildren(indexes[row], indexes[column]);
 			
 			//parents
-			tree[indexes[row]].setParent(numGroups + i);
-			tree[indexes[column]].setParent(numGroups + i);
+			tree[indexes[row]].setParent(numLeaves + i);
+			tree[indexes[column]].setParent(numLeaves + i);
 			
 			//blength = distance / 2;
 			float blength = ((1.0 - largest) / 2);
@@ -168,12 +166,12 @@ Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
 			tree[indexes[column]].setBranchLength(blength - tree[indexes[column]].getLengthToLeaves());
 			
 			//set your length to leaves to your childs length plus branchlength
-			tree[numGroups + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
+			tree[numLeaves + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
 			
 			
 			//update index 
-			indexes[row] = numGroups+i;
-			indexes[column] = numGroups+i;
+			indexes[row] = numLeaves+i;
+			indexes[column] = numLeaves+i;
 			
 			//remove highest value that caused the merge.
 			sims[row][column] = -1000.0;
@@ -590,6 +588,37 @@ int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
 	}
 }
 /*****************************************************************/
+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 branch length
+			tree[i].setBranchLength(copy->tree[i].getBranchLength());
+            
+			//copy parent
+			tree[i].setParent(copy->tree[i].getParent());
+            
+			//copy children
+			tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
+        }
+		
+        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++) {
+			if (m->control_pressed) { break; }
+            
+			tree[i].pGroups = (mergeGroups(i));
+			tree[i].pcount = (mergeGcounts(i));
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "getCopy");
+		exit(1);
+	}
+}
+/*****************************************************************/
 void Tree::getCopy(Tree* copy) {
 	try {