moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 8e459810589cbc23e9f443884406028382e4e212..14d86e6daf211b625931c3d52a127cd441086267 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -78,7 +78,7 @@ void Tree::addNamesToCounts() {
                        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;
@@ -292,14 +292,14 @@ 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 +381,8 @@ 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 +542,10 @@ 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 +643,7 @@ 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;