made read.tree not require a groupfile, if one is not given all seqs are assumed...

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 7da3cef3718502640d61377bccbaae0d8e4213d3..3cb26113f8deb8acf3bf28f7040becf2bac7385f 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -9,7 +9,19 @@
 
 #include "tree.h"
 
-
+/*****************************************************************/
+Tree::Tree(string g) {
+       try {
+               globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
+               
+               parseTreeFile();  globaldata->runParse = false;  
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Tree", "Tree - just parse");
+               exit(1);
+       }
+}
 /*****************************************************************/
 Tree::Tree() {
        try {
@@ -69,15 +81,19 @@ void Tree::addNamesToCounts() {
 
                                
                //go through each leaf and update its pcounts and pgroups
+               
+               //float A = clock();
+
                for (int i = 0; i < numLeaves; i++) {
+
                        string name = tree[i].getName();
-                       
+               
                        map<string, string>::iterator itNames = globaldata->names.find(name);
-                       
+               
                        if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
                        else {
                                vector<string> dupNames;
-                               splitAtComma(globaldata->names[name], dupNames);
+                               m->splitAtComma(globaldata->names[name], dupNames);
                                
                                map<string, int>::iterator itCounts;
                                int maxPars = 1;
@@ -131,8 +147,11 @@ void Tree::addNamesToCounts() {
                                tree[i].setGroup(nodeGroups);
                                
                        }//end else
-               }//end for
-                               
+               }//end for              
+               
+               //float B = clock();
+               //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;     
+
        }
        catch(exception& e) {
                m->errorOut(e, "Tree", "addNamesToCounts");
@@ -168,7 +187,8 @@ void Tree::setIndex(string searchName, int index) {
 /*****************************************************************/
 int Tree::assembleTree() {
        try {
-       
+               //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();  }
                
@@ -179,7 +199,8 @@ int Tree::assembleTree() {
                        tree[i].pGroups = (mergeGroups(i));
                        tree[i].pcount = (mergeGcounts(i));
                }
-               
+               //float B = clock();
+               //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
                return 0;
        }
        catch(exception& e) {
@@ -292,14 +313,14 @@ map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
                
                //loop through nodes groups removing the ones the user doesn't want
                for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
-                               if (inUsersGroups(it->first, g) != true) {
+                               if (m->inUsersGroups(it->first, g) != true) {
                                        tree[lc].pGroups.erase(it++);
                                }else { it++; }
                }
 
                //loop through nodes groups removing the ones the user doesn't want
                for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
-                               if (inUsersGroups(it->first, g) != true) {
+                               if (m->inUsersGroups(it->first, g) != true) {
                                        tree[rc].pGroups.erase(it++);
                                }else { it++; }
                }
@@ -381,8 +402,8 @@ void Tree::randomLabels(vector<string> g) {
                        //if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
                        bool treez, treei;
                
-                       treez = inUsersGroups(tree[z].getGroup(), g);
-                       treei = inUsersGroups(tree[i].getGroup(), g);
+                       treez = m->inUsersGroups(tree[z].getGroup(), g);
+                       treei = m->inUsersGroups(tree[i].getGroup(), g);
                        
                        if ((treez == true) && (treei == true)) {
                                //switches node i and node z's info.
@@ -542,10 +563,10 @@ void Tree::printForBoot(ostream& out) {
 void Tree::createNewickFile(string f) {
        try {
                int root = findRoot();
-               //filename = getRootName(globaldata->getTreeFile()) + "newick";
+               //filename = m->getRootName(globaldata->getTreeFile()) + "newick";
                filename = f;
 
-               openOutputFile(filename, out);
+               m->openOutputFile(filename, out);
                
                printBranch(root, out, "branch");
                
@@ -643,7 +664,7 @@ void Tree::parseTreeFile() {
        try {
                string filename = globaldata->getTreeFile();
                ifstream filehandle;
-               openInputFile(filename, filehandle);
+               m->openInputFile(filename, filehandle);
                int c, comment;
                comment = 0;
                int done = 1;
@@ -713,6 +734,10 @@ void Tree::parseTreeFile() {
                        }
                }
                filehandle.close();
+               
+               //for (int i = 0; i < globaldata->Treenames.size(); i++) {
+//cout << globaldata->Treenames[i] << endl; }
+//cout << globaldata->Treenames.size() << endl;
        }
        catch(exception& e) {
                m->errorOut(e, "Tree", "parseTreeFile");