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

[mothur.git] / phylotree.cpp

diff --git a/phylotree.cpp b/phylotree.cpp
index 2ea219350c1f8bf8099b7cfc40d28ddcdfc9d872..1fd4e5d238119bbcd6be5c54fbd7013fcdfc27bd 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -55,24 +55,24 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
                        delete buffer;
                        
                        //read version
-                       getline(iss); gobble(iss);
+                       m->getline(iss); m->gobble(iss);
                        
-                       iss >> numNodes; gobble(iss);
+                       iss >> numNodes; m->gobble(iss);
                        
                        tree.resize(numNodes);
                        
                        for (int i = 0; i < tree.size(); i++) {
-                               iss >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(iss);
+                               iss >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(iss);
                        }
                        
                        //read genus nodes
                        int numGenus = 0;
-                       iss >> numGenus; gobble(iss);
+                       iss >> numGenus; m->gobble(iss);
                        
                        int gnode, gsize;
                        totals.clear();
                        for (int i = 0; i < numGenus; i++) {
-                               iss >> gnode >> gsize; gobble(iss);
+                               iss >> gnode >> gsize; m->gobble(iss);
                                
                                uniqueTaxonomies[gnode] = gnode;
                                totals.push_back(gsize);
@@ -82,24 +82,24 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
                        
                #else
                        //read version
-                       string line = getline(in); gobble(in);
+                       string line = m->getline(in); m->gobble(in);
                        
-                       in >> numNodes; gobble(in);
+                       in >> numNodes; m->gobble(in);
                        
                        tree.resize(numNodes);
                        
                        for (int i = 0; i < tree.size(); i++) {
-                               in >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(in);
+                               in >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(in);
                        }
                        
                        //read genus nodes
                        int numGenus = 0;
-                       in >> numGenus; gobble(in);
+                       in >> numGenus; m->gobble(in);
                        
                        int gnode, gsize;
                        totals.clear();
                        for (int i = 0; i < numGenus; i++) {
-                               in >> gnode >> gsize; gobble(in);
+                               in >> gnode >> gsize; m->gobble(in);
                                
                                uniqueTaxonomies[gnode] = gnode;
                                totals.push_back(gsize);
@@ -144,7 +144,7 @@ PhyloTree::PhyloTree(string tfile){
                        MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 
                        if (pid == 0) {
-                               positions = setFilePosEachLine(tfile, num);
+                               positions = m->setFilePosEachLine(tfile, num);
                                
                                //send file positions to all processes
                                for(int i = 1; i < processors; i++) { 
@@ -179,11 +179,11 @@ PhyloTree::PhyloTree(string tfile){
                
                #else
                        ifstream in;
-                       openInputFile(tfile, in);
+                       m->openInputFile(tfile, in);
                        
                        //read in users taxonomy file and add sequences to tree
                        while(!in.eof()){
-                               in >> name >> tax; gobble(in);
+                               in >> name >> tax; m->gobble(in);
                        
                                addSeqToTree(name, tax);
                        }
@@ -365,7 +365,7 @@ void PhyloTree::binUnclassified(string file){
        try {
        
                ofstream out;
-               openOutputFile(file, out);
+               m->openOutputFile(file, out);
                
                map<string, int>::iterator itBin;
                map<string, int>::iterator childPointer;
@@ -519,7 +519,7 @@ void PhyloTree::printTreeNodes(string treefilename) {
                #endif
 
                        ofstream outTree;
-                       openOutputFile(treefilename, outTree);
+                       m->openOutputFile(treefilename, outTree);
                        
                        //output mothur version
                        outTree << "#" << m->getVersion() << endl;