X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=c805edc9896bf15b4e7397305c13d8bfbce175d8;hb=cad05a21b084833b07808c1586e755be48fe7e1a;hp=3062f6677fa8527b4eb59a9ab979458465bfb777;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index 3062f66..c805edc 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -230,7 +230,7 @@ int ReadNewickTree::readTreeString() {
 
 			lc = readNewickInt(filehandle, n, T);
 			if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
-		
+	
 			if(filehandle.peek()==','){							
 				readSpecialChar(filehandle,',',"comma");
 			}
@@ -287,21 +287,62 @@ 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
-			readSpecialChar(f,',',"comma");
+		
+			//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++;
+			}
+			
+			//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");	
 				//to pass over labels in trees
 				c=filehandle.get();
 				while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
 				filehandle.putback(c);
-
 			}			
 		
 			if(f.peek() == ':'){									      
@@ -313,12 +354,55 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			}else{
 				T->tree[n].setBranchLength(0.0); 
 			}						
+			
+			//to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
+			/*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);
+				T->tree[rc].setParent(n);
+				
+				T->printTree(); cout << endl;
+				lc = n;
+				n++;
+				
+				readSpecialChar(f,',',"comma");
+
+				rc = readNewickInt(f, n, T);
 		
-			T->tree[n].setChildren(lc,rc);
-			T->tree[lc].setParent(n);
-			T->tree[rc].setParent(n);
+				if (rc == -1) { return -1; }  //reports an error in reading	
+				
+				if(f.peek()==')'){	
+					readSpecialChar(f,')',"right parenthesis");	
+					//to pass over labels in trees
+					c=filehandle.get();
+					while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+					filehandle.putback(c);
+					
+					if(f.peek() == ':'){									      
+						readSpecialChar(f,':',"colon");	
+					
+						if(n >= numNodes){	m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
+					
+						T->tree[n].setBranchLength(readBranchLength(f));
+					}else{
+						T->tree[n].setBranchLength(0.0); 
+					}						
+
+					break;
+				}			
+			}*/
 		
+			//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 = "";
@@ -327,7 +411,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 				name += d;
 				d=f.get();
 			}
-		
+		cout << name << endl;
 			int blen = 0;
 			if(d == ':')	{		blen = 1;	}