removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 02f400407cfaa5f8c9283fa4f96d8bbc2fb0c3d8..53aa4025bef940b9d3fcb830e6686760338ee8ef 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -10,9 +10,8 @@
 #include "tree.h"
 
 /*****************************************************************/
-Tree::Tree(int num) {
+Tree::Tree(int num, TreeMap* t) : tmap(t) {
        try {
-               globaldata = GlobalData::getInstance();
                m = MothurOut::getInstance();
                
                numLeaves = num;  
@@ -26,12 +25,13 @@ Tree::Tree(int num) {
        }
 }
 /*****************************************************************/
-Tree::Tree(string g) {
+Tree::Tree(string g) { //do not use tree generated by this its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
        try {
-               globaldata = GlobalData::getInstance();
                m = MothurOut::getInstance();
                
-               parseTreeFile();  globaldata->runParse = false;  
+               tmap = NULL;
+               
+               parseTreeFile();  m->runParse = false;  
        }
        catch(exception& e) {
                m->errorOut(e, "Tree", "Tree - just parse");
@@ -39,31 +39,30 @@ Tree::Tree(string g) {
        }
 }
 /*****************************************************************/
-Tree::Tree() {
+Tree::Tree(TreeMap* t) : tmap(t) {
        try {
-               globaldata = GlobalData::getInstance();
                m = MothurOut::getInstance();
                
-               if (globaldata->runParse == true) {  parseTreeFile();  globaldata->runParse = false;  }
+               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 = globaldata->Treenames.size();
+               numLeaves = m->Treenames.size();
                numNodes = 2*numLeaves - 1;
                
                tree.resize(numNodes);
                        
                //initialize groupNodeInfo
-               for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
-                       groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+               for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+                       groupNodeInfo[tmap->namesOfGroups[i]].resize(0);
                }
                
                //initialize tree with correct number of nodes, name and group info.
                for (int i = 0; i < numNodes; i++) {
                        //initialize leaf nodes
                        if (i <= (numLeaves-1)) {
-                               tree[i].setName(globaldata->Treenames[i]);
+                               tree[i].setName(m->Treenames[i]);
                                
                                //save group info
-                               string group = globaldata->gTreemap->getGroup(globaldata->Treenames[i]);
+                               string group = tmap->getGroup(m->Treenames[i]);
                                
                                vector<string> tempGroups; tempGroups.push_back(group);
                                tree[i].setGroup(tempGroups);
@@ -74,7 +73,7 @@ Tree::Tree() {
                                tree[i].pGroups[group] = 1;
                                
                                //Treemap knows name, group and index to speed up search
-                               globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
+                               tmap->setIndex(m->Treenames[i], i);
        
                        //intialize non leaf nodes
                        }else if (i > (numLeaves-1)) {
@@ -117,19 +116,19 @@ void Tree::addNamesToCounts() {
 
                        string name = tree[i].getName();
                
-                       map<string, string>::iterator itNames = globaldata->names.find(name);
+                       map<string, string>::iterator itNames = m->names.find(name);
                
-                       if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
+                       if (itNames == m->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
                        else {
                                vector<string> dupNames;
-                               m->splitAtComma(globaldata->names[name], dupNames);
+                               m->splitAtComma(m->names[name], dupNames);
                                
                                map<string, int>::iterator itCounts;
                                int maxPars = 1;
                                set<string> groupsAddedForThisNode;
                                for (int j = 0; j < dupNames.size(); j++) {
                                        
-                                       string group = globaldata->gTreemap->getGroup(dupNames[j]);
+                                       string group = tmap->getGroup(dupNames[j]);
                                        
                                        if (dupNames[j] != name) {//you already added yourself in the constructor
                                
@@ -196,7 +195,7 @@ int Tree::getIndex(string searchName) {
        try {
                //Treemap knows name, group and index to speed up search
                // getIndex function will return the vector index or -1 if seq is not found.
-               int index = globaldata->gTreemap->getIndex(searchName);
+               int index = tmap->getIndex(searchName);
                return index;
                
        }
@@ -210,7 +209,7 @@ int Tree::getIndex(string searchName) {
 void Tree::setIndex(string searchName, int index) {
        try {
                //set index in treemap
-               globaldata->gTreemap->setIndex(searchName, index);
+               tmap->setIndex(searchName, index);
        }
        catch(exception& e) {
                m->errorOut(e, "Tree", "setIndex");
@@ -223,7 +222,7 @@ int Tree::assembleTree() {
                //float A = clock();
 
                //if user has given a names file we want to include that info in the pgroups and pcount info.
-               if(globaldata->names.size() != 0) {  addNamesToCounts();  }
+               if(m->names.size() != 0) {  addNamesToCounts();  }
                
                //build the pGroups in non leaf nodes to be used in the parsimony calcs.
                for (int i = numLeaves; i < numNodes; i++) {
@@ -274,7 +273,7 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                tree[i].setName(Groups[i]);
                                
                                //save group info
-                               string group = globaldata->gTreemap->getGroup(Groups[i]);
+                               string group = tmap->getGroup(Groups[i]);
                                vector<string> tempGroups; tempGroups.push_back(group);
                                tree[i].setGroup(tempGroups);
                                groupNodeInfo[group].push_back(i); 
@@ -284,7 +283,7 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                tree[i].pGroups[group] = 1;
                                
                                //Treemap knows name, group and index to speed up search
-                               globaldata->gTreemap->setIndex(Groups[i], i);
+                               tmap->setIndex(Groups[i], i);
                                
                                //intialize non leaf nodes
                        }else if (i > (numLeaves-1)) {
@@ -436,7 +435,7 @@ int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
                        
                        return (index++);
                }else { //you are a leaf
-                       int indexInNewTree = globaldata->gTreemap->getIndex(oldtree[node].getName());
+                       int indexInNewTree = tmap->getIndex(oldtree[node].getName());
                        return indexInNewTree;
                }
        }
@@ -633,8 +632,8 @@ void Tree::randomLabels(vector<string> g) {
        try {
        
                //initialize groupNodeInfo
-               for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
-                       groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+               for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+                       groupNodeInfo[tmap->namesOfGroups[i]].resize(0);
                }
                
                for(int i = 0; i < numLeaves; i++){
@@ -875,7 +874,7 @@ try {
                                }
                        }
                }else { //you are a leaf
-                       string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
+                       string leafGroup = tmap->getGroup(tree[node].getName());
                        
                        if (mode == "branch") {
                                out << leafGroup; 
@@ -938,7 +937,7 @@ void Tree::printBranch(int node, ostream& out, string mode, vector<Node>& theseN
                                }
                        }
                }else { //you are a leaf
-                       string leafGroup = globaldata->gTreemap->getGroup(theseNodes[node].getName());
+                       string leafGroup = tmap->getGroup(theseNodes[node].getName());
                        
                        if (mode == "branch") {
                                out << leafGroup; 
@@ -987,7 +986,7 @@ void Tree::parseTreeFile() {
        
        //only takes names from the first tree and assumes that all trees use the same names.
        try {
-               string filename = globaldata->getTreeFile();
+               string filename = m->getTreeFile();
                ifstream filehandle;
                m->openInputFile(filename, filehandle);
                int c, comment;
@@ -1053,9 +1052,9 @@ void Tree::parseTreeFile() {
                                        //c = , until done with translation then c = ;
                                        h = name.substr(name.length()-1, name.length()); 
                                        name.erase(name.end()-1);  //erase the comma
-                                       globaldata->Treenames.push_back(number);
+                                       m->Treenames.push_back(number);
                                }
-                               if(number == ";") { globaldata->Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
+                               if(number == ";") { m->Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
                        }
                }
                filehandle.close();
@@ -1102,7 +1101,7 @@ int Tree::readTreeString(ifstream& filehandle)    {
                                }
                                
 //cout << "name = " << name << endl;
-                               globaldata->Treenames.push_back(name);
+                               m->Treenames.push_back(name);
                                filehandle.putback(c);
 //k = c;
 //cout << " after putback" <<  k << endl;