added get.groups and remove.groups commands

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 1dd77f9152b241321f6658d0e0efc025c01a1a71..e98524b45e9ec513fe171c5a342ab381a68fcacc 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -25,7 +25,7 @@ ReadTree::ReadTree() {
 int ReadTree::readSpecialChar(istream& f, char c, string name) {
     try {
        
-               gobble(f);
+               m->gobble(f);
                char d = f.get();
        
                if(d == EOF){
@@ -37,7 +37,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
                        exit(1);
                }
                if(d == ')' && f.peek() == '\n'){
-                       gobble(f);
+                       m->gobble(f);
                }       
                return d;
        }
@@ -51,7 +51,7 @@ int ReadTree::readSpecialChar(istream& f, char c, string name) {
 int ReadTree::readNodeChar(istream& f) {
        try {
 //             while(isspace(d=f.get()))               {;}
-               gobble(f);
+               m->gobble(f);
                char d = f.get();
 
                if(d == EOF){
@@ -76,7 +76,7 @@ float ReadTree::readBranchLength(istream& f) {
                        m->mothurOut("Error: Missing branch length in input tree.\n");
                        exit(1);
                }
-               gobble(f);
+               m->gobble(f);
                return b;
        }
        catch(exception& e) {
@@ -125,7 +125,7 @@ int ReadNewickTree::read() {
                                
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
-                               gobble(filehandle);
+                               m->gobble(filehandle);
                        }
                //if you are a nexus file
                }else if ((c = filehandle.peek()) == '#') {
@@ -341,7 +341,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        if(f.peek() == ':'){                                                                          
                                readSpecialChar(f,':',"colon"); 
                                                                                
-                               if(n >= numNodes){      m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
+                               if(n >= numNodes){ m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
                                
                                T->tree[n].setBranchLength(readBranchLength(f));
                        }else{