fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 2cd9cbabc691d692fcb30a7fb9408da8ad22c383..6aa1b829c91d59bcee681b906c6c31ab07f1c168 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -13,9 +13,9 @@
 /*****************************************************************/
 Tree::Tree() {
        try {
-       
                globaldata = GlobalData::getInstance();
-               numLeaves = globaldata->gTreemap->getNumSeqs();
+               
+               numLeaves = globaldata->Treenames.size();
                numNodes = 2*numLeaves - 1;
                
                tree.resize(numNodes);
@@ -24,13 +24,13 @@ Tree::Tree() {
                for (int i = 0; i < numNodes; i++) {
                        //initialize leaf nodes
                        if (i <= (numLeaves-1)) {
-                               tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
-                               tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
+                               tree[i].setName(globaldata->Treenames[i]);
+                               tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
                                //set pcount and pGroup for groupname to 1.
-                               tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
-                               tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
+                               tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
+                               tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
                                //Treemap knows name, group and index to speed up search
-                               globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+                               globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
        
                        //intialize non leaf nodes
                        }else if (i > (numLeaves-1)) {
@@ -49,6 +49,8 @@ Tree::Tree() {
        }               
 }
 
+/*****************************************************************/
+Tree::~Tree() {}
 /*****************************************************************/
 int Tree::getIndex(string searchName) {
        try {
@@ -178,7 +180,7 @@ map<string, int> Tree::mergeGroups(int i) {
                        for(it=parsimony.begin();it!=parsimony.end();it++){
                                if(it->second == 1){
                                        parsimony.erase(it->first);
-                                       it--;
+//                                     it--;
                                }
                        }
                        //set one remaining groups to 1
@@ -240,24 +242,20 @@ map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
                                maxPars = parsimony[it->first];
                        }
                }
-       
+                       
                // this is true if right child had a greater parsimony for a certain group
                if(maxPars > 1){
                        //erase all the groups that are only 1 because you found something with 2.
                        for(it=parsimony.begin();it!=parsimony.end();it++){
                                if(it->second == 1){
                                        parsimony.erase(it->first);
-                                       it--;
                                }
                        }
-                       //set one remaining groups to 1
-                       //so with our above example p[white] = 2 would be left and it would become p[white] = 1
                        for(it=parsimony.begin();it!=parsimony.end();it++){
                                parsimony[it->first] = 1;
                        }
+               }               
                
-               }
-       
                return parsimony;
        }
        catch(exception& e) {
@@ -488,7 +486,7 @@ int Tree::findRoot() {
        try {
                for (int i = 0; i < numNodes; i++) {
                        //you found the root
-                       if (tree[i].getParent() == -1) { return i; }
+                       if (tree[i].getParent() == -1) { return i; }  
                }
                return -1;
        }