X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=c805edc9896bf15b4e7397305c13d8bfbce175d8;hb=cad05a21b084833b07808c1586e755be48fe7e1a;hp=1df49b5502f405bf29b31ee585fb5d6a264f9cda;hpb=6de5adaae66b28aa60a75f123005cede410c156c;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index 1df49b5..c805edc 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -287,15 +287,55 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 		if (m->control_pressed) { return -1; } 
 		
 		int c = readNodeChar(f);
-    
+  string k;
+k = c;
+	cout << "at beginning = " << k <<endl;  
 		if(c == '('){
-			int lc = readNewickInt(f, n, T);
-			if (lc == -1) { return -1; } //reports an error in reading
+		
+			//to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
+			//read all children
+			vector<int> childrenNodes;
+			while(f.peek() != ')'){
+				int child = readNewickInt(f, n, T);
+				if (child == -1) { return -1; } //reports an error in reading
+				
+				childrenNodes.push_back(child);
+				
+				//after a child you either have , or ), check for both
+				if(f.peek()==')'){  break;  }
+				else if (f.peek()==',') {   readSpecialChar(f,',',"comma");  }
+				else { string k;
+			k = f.peek();
+	cout << "in here k = " << k << '\t' << f.tellg() <<endl;
+ }
+			}
+	cout << childrenNodes.size() << endl;		
+			if (childrenNodes.size() < 2) {  m->mothurOut("Error in tree, please correct."); m->mothurOutEndLine(); return -1; }
+			
+			//then force into 2 node structure
+			for (int i = 1; i < childrenNodes.size(); i++) {
+			
+				int lc, rc;
+				if (i == 1) { lc = childrenNodes[i-1]; rc = childrenNodes[i]; }
+				else { lc = n; rc = childrenNodes[i]; }
+			cout << i << '\t' << lc << '\t' << rc << endl;	
+				T->tree[n].setChildren(lc,rc);
+				T->tree[lc].setParent(n);
+				T->tree[rc].setParent(n);
+				
+				T->printTree(); cout << endl;
+				n++;
+			}
 			
-			readSpecialChar(f,',',"comma");
+			//to account for extra ++ in looping
+			n--;
+			//int lc = readNewickInt(f, n, T);
+			//if (lc == -1) { return -1; } //reports an error in reading
+			
+			//readSpecialChar(f,',',"comma");
 
-			int rc = readNewickInt(f, n, T);
-			if (rc == -1) { return -1; }  //reports an error in reading	
+			//int rc = readNewickInt(f, n, T);
+			//if (rc == -1) { return -1; }  //reports an error in reading	
 			
 			if(f.peek()==')'){	
 				readSpecialChar(f,')',"right parenthesis");	
@@ -303,7 +343,6 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 				c=filehandle.get();
 				while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
 				filehandle.putback(c);
-
 			}			
 		
 			if(f.peek() == ':'){									      
@@ -317,8 +356,10 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			}						
 			
 			//to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
-			while(f.peek() == ','){
-				
+			/*while(f.peek() == ','){
+			string k;
+			k = f.peek();
+	cout << "in here k = " << k << '\t' << f.tellg() <<endl;
 				//force this node to be left child and read new rc
 				T->tree[n].setChildren(lc,rc);
 				T->tree[lc].setParent(n);
@@ -330,14 +371,11 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 				
 				readSpecialChar(f,',',"comma");
 
-				int rc = readNewickInt(f, n, T);
-		cout << n << '\t' << lc << '\t' << rc << endl;
+				rc = readNewickInt(f, n, T);
+		
 				if (rc == -1) { return -1; }  //reports an error in reading	
 				
 				if(f.peek()==')'){	
-				string k;
-				k = f.peek();
-		cout << "in here " << k << endl;
 					readSpecialChar(f,')',"right parenthesis");	
 					//to pass over labels in trees
 					c=filehandle.get();
@@ -345,25 +383,26 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 					filehandle.putback(c);
 					
 					if(f.peek() == ':'){									      
-					readSpecialChar(f,':',"colon");	
+						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));
+						T->tree[n].setBranchLength(readBranchLength(f));
 					}else{
 						T->tree[n].setBranchLength(0.0); 
 					}						
 
 					break;
 				}			
-			}
-	cout << n << '\t' << lc << '\t' << rc << endl;		
-			T->tree[n].setChildren(lc,rc);
-			T->tree[lc].setParent(n);
-			T->tree[rc].setParent(n);
-			T->printTree();  cout << endl;
+			}*/
+		
+			//T->tree[n].setChildren(lc,rc);
+			//T->tree[lc].setParent(n);
+			//T->tree[rc].setParent(n);
+			//T->printTree();  cout << endl;
 			
 			return n++;
+		
 		}else{
 			f.putback(c);
 			string name = "";