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

[mothur.git] / phylosummary.cpp

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 870f35fa3b994a78ed165d1179c8ee2d6daf207b..39bfdf3dfecb1cd4aaecb2763043d0c8cbb00d29 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -48,12 +48,12 @@ void PhyloSummary::summarize(string userTfile){
        try {
                
                ifstream in;
-               openInputFile(userTfile, in);
+               m->openInputFile(userTfile, in);
                
                //read in users taxonomy file and add sequences to tree
                string name, tax;
                while(!in.eof()){
-                       in >> name >> tax; gobble(in);
+                       in >> name >> tax; m->gobble(in);
                        
                        addSeqToTree(name, tax);
                        
@@ -252,15 +252,15 @@ void PhyloSummary::readTreeStruct(ifstream& in){
        try {
        
                //read version
-               string line = getline(in); gobble(in);
+               string line = m->getline(in); m->gobble(in);
                
                int num;
                
-               in >> num; gobble(in);
+               in >> num; m->gobble(in);
                
                tree.resize(num);
                
-               in >> maxLevel; gobble(in);
+               in >> maxLevel; m->gobble(in);
        
                //read the tree file
                for (int i = 0; i < tree.size(); i++) {
@@ -284,7 +284,7 @@ void PhyloSummary::readTreeStruct(ifstream& in){
                        
                        tree[i].total = 0;
                        
-                       gobble(in);
+                       m->gobble(in);
                        
                        //if (tree[i].level > maxLevel) {  maxLevel = tree[i].level;  }
                }