X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=e98524b45e9ec513fe171c5a342ab381a68fcacc;hb=1d5962b46d9e72a2b855b4176d1c47df9a163fac;hp=1dd77f9152b241321f6658d0e0efc025c01a1a71;hpb=28d6f2bddc5c0718ae7f63648be3130a35fb0f02;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index 1dd77f9..e98524b 100644
--- 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{