added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 642c6658739dd5252b2d61083ce6af2b872785ec..e138121661f19f77d1c8603036793f86a95dfe67 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);
@@ -24,22 +24,18 @@ 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]));
-                               //the node knows its index
-                               tree[i].setIndex(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)) {
                                tree[i].setName("");
                                tree[i].setGroup("");
-                               //the node knows its index
-                               tree[i].setIndex(i);
                        }
                }
        }
@@ -54,7 +50,8 @@ Tree::Tree() {
 }
 
 /*****************************************************************/
-
+Tree::~Tree() {}
+/*****************************************************************/
 int Tree::getIndex(string searchName) {
        try {
                //Treemap knows name, group and index to speed up search
@@ -157,7 +154,7 @@ map<string, int> Tree::mergeGroups(int i) {
        try {
                int lc = tree[i].getLChild();
                int rc = tree[i].getRChild();
-               
+
                //set parsimony groups to left child
                map<string,int> parsimony = tree[lc].pGroups;
                
@@ -183,7 +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
@@ -245,24 +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) {
@@ -460,7 +453,22 @@ void Tree::randomTopology() {
                exit(1);
        }               
 }
-
+/*****************************************************************/
+void Tree::print(ostream& out) {
+       try {
+               int root = findRoot();
+               printBranch(root, out);
+               out << ";" << endl;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Tree class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+}
 /*****************************************************************/
 // This prints out the tree in Newick form.
 void Tree::createNewickFile(string f) {
@@ -470,7 +478,7 @@ void Tree::createNewickFile(string f) {
                filename = f;
                openOutputFile(filename, out);
                
-               printBranch(root);
+               printBranch(root, out);
                
                // you are at the end of the tree
                out << ";" << endl;
@@ -493,7 +501,7 @@ 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;
        }
@@ -508,18 +516,26 @@ int Tree::findRoot() {
 }
 
 /*****************************************************************/
-void Tree::printBranch(int node) {
+void Tree::printBranch(int node, ostream& out) {
        try {
                
                // you are not a leaf
                if (tree[node].getLChild() != -1) {
                        out << "(";
-                       printBranch(tree[node].getLChild());
+                       printBranch(tree[node].getLChild(), out);
                        out << ",";
-                       printBranch(tree[node].getRChild());
+                       printBranch(tree[node].getRChild(), out);
                        out << ")";
+                       //if there is a branch length then print it
+                       if (tree[node].getBranchLength() != -1) {
+                               out << ":" << tree[node].getBranchLength();
+                       }
                }else { //you are a leaf
-                       out << tree[node].getGroup() << ":" << tree[node].getBranchLength();
+                       out << tree[node].getGroup(); 
+                       //if there is a branch length then print it
+                       if (tree[node].getBranchLength() != -1) {
+                               out << ":" << tree[node].getBranchLength();
+                       }
                }
                
        }