X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=400a72ae388a88c5b94aa2b8a717471f600b33ed;hb=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c;hp=8e459810589cbc23e9f443884406028382e4e212;hpb=4d7ffb38e091e9e7425d94e112551a3f90cacb0f;p=mothur.git

diff --git a/tree.cpp b/tree.cpp
index 8e45981..400a72a 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -736,39 +736,20 @@ int Tree::readTreeString(ifstream& filehandle)	{
 //cout << " at beginning of while " <<  k << endl;			
 			if(c == ')')  {    
 				//to pass over labels in trees
-				c=filehandle.get();
-				while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
-				filehandle.putback(c);
+				string label = readLabel(filehandle);
 			}
+			
 			if(c == ';') { return 0; }
 			if(c == -1) { return 0; }
+			
 			//if you are a name
 			if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
-				name = "";
-				c = filehandle.get();
-			//k = c;
-//cout << k << endl;
-				while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {			
-					name += c;
-					c = filehandle.get();
-			//k = c;
-//cout << " in name while " << k << endl;
-				}
-				
-//cout << "name = " << name << endl;
+				name = readName(filehandle);
 				globaldata->Treenames.push_back(name);
-				filehandle.putback(c);
-//k = c;
-//cout << " after putback" <<  k << endl;
 			} 
 			
 			if(c  == ':') { //read until you reach the end of the branch length
-				while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
-					c = filehandle.get();
-	//k = c;
-	//cout << " in branch while " << k << endl;
-				}
-				filehandle.putback(c);
+				string bl = readBranchLength(filehandle);
 			}
 		
 			c = filehandle.get();
@@ -789,6 +770,68 @@ int Tree::readTreeString(ifstream& filehandle)	{
 }	
 
 /*******************************************************/
+string Tree::readLabel(ifstream& filehandle)	{
+	try {
+		
+		string label = "";
+		
+		//to pass over labels in trees
+		int c=filehandle.get();
+		while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ label += c; c=filehandle.get(); }
+		filehandle.putback(c);
+		
+		return label;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "readLabel");
+		exit(1);
+	}
+}	
+/*******************************************************/
+string Tree::readName(ifstream& filehandle)	{
+	try {
+		
+		string name = "";
+		int c = filehandle.get();
+		
+		while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {			
+			name += c;
+			c = filehandle.get();
+		}
+				
+//cout << "name = " << name << endl;
+		filehandle.putback(c);
+		
+		return name;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "readName");
+		exit(1);
+	}
+}	
+/*******************************************************/
+string Tree::readBranchLength(ifstream& filehandle)	{
+	try {
+		
+		string br = "";
+		int c;
+		while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+			br += c;
+			c = filehandle.get();
+		}
+		filehandle.putback(c);
+		
+		return br;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Tree", "readBranchLength");
+		exit(1);
+	}
+}	
 
 /*******************************************************/
+/*******************************************************/